NM_001102597.3:c.1106C>T

Variant names:

• chr19-44517149-G-A
• rs10414398
• NM_001102597.3:c.1106C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001102597.3(CEACAM20):​c.1106C>T​(p.Ser369Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,613,276 control chromosomes in the GnomAD database, including 11,302 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (2124 hom., cov: 31)
  • Exomes 𝑓: 0.099 (9178 hom.)
• Consequence: CEACAM20 NM_001102597.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 17 publications found

Genes affected

CEACAM20 (HGNC:24879): (CEA cell adhesion molecule 20) Predicted to be involved in positive regulation of cytokine production. Predicted to act upstream of or within response to bacterium. Predicted to be located in apical plasma membrane and microvillus membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.005539626).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102597.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM20	NM_001102597.3	MANE Select	c.1106C>T	p.Ser369Phe	missense	Exon 6 of 12	NP_001096067.2
	CEACAM20	NM_001102600.3		c.1106C>T	p.Ser369Phe	missense	Exon 6 of 11	NP_001096070.2
	CEACAM20	NM_001102599.3		c.1030+3325C>T		intron	N/A	NP_001096069.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM20	ENST00000614924.5	TSL:1 MANE Select	c.1106C>T	p.Ser369Phe	missense	Exon 6 of 12	ENSP00000481937.1
	CEACAM20	ENST00000621342.4	TSL:1	c.1106C>T	p.Ser369Phe	missense	Exon 6 of 12	ENSP00000480940.1
	CEACAM20	ENST00000611497.4	TSL:1	c.1106C>T	p.Ser369Phe	missense	Exon 6 of 11	ENSP00000483912.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21990 AN: 151918 Hom.: 2120 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.158

GnomAD2 exomes AF: 0.135 AC: 33566 AN: 248560 AF XY: 0.129

Gnomad AFR exome AF: 0.249

Gnomad AMR exome AF: 0.279

Gnomad ASJ exome AF: 0.136

Gnomad EAS exome AF: 0.138

Gnomad FIN exome AF: 0.0371

Gnomad NFE exome AF: 0.0841

Gnomad OTH exome AF: 0.126

GnomAD4 exome AF: 0.0993 AC: 145074 AN: 1461240 Hom.: 9178 Cov.: 33 AF XY: 0.100 AC XY: 73044 AN XY: 726892

African (AFR) AF: 0.251 AC: 8395 AN: 33478

American (AMR) AF: 0.272 AC: 12158 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 3523 AN: 26136

East Asian (EAS) AF: 0.138 AC: 5494 AN: 39700

South Asian (SAS) AF: 0.168 AC: 14524 AN: 86234

European-Finnish (FIN) AF: 0.0377 AC: 1999 AN: 53032

Middle Eastern (MID) AF: 0.162 AC: 936 AN: 5768

European-Non Finnish (NFE) AF: 0.0816 AC: 90779 AN: 1111822

Other (OTH) AF: 0.120 AC: 7266 AN: 60372

GnomAD4 genome AF: 0.145 AC: 22019 AN: 152036 Hom.: 2124 Cov.: 31 AF XY: 0.146 AC XY: 10814 AN XY: 74318

African (AFR) AF: 0.247 AC: 10213 AN: 41406

American (AMR) AF: 0.217 AC: 3309 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.146 AC: 753 AN: 5164

South Asian (SAS) AF: 0.164 AC: 789 AN: 4816

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10614

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5562 AN: 67990

Other (OTH) AF: 0.159 AC: 334 AN: 2104

Alfa AF: 0.108 Hom.: 4716

Bravo AF: 0.165

TwinsUK AF: 0.0836 AC: 310

ALSPAC AF: 0.0885 AC: 341

ESP6500AA AF: 0.228 AC: 966

ESP6500EA AF: 0.0825 AC: 699

ExAC AF: 0.131 AC: 15806

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.35
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	22
DANN	Benign	0.78
DEOGEN2	Benign	0.17	T
FATHMM_MKL	Benign	0.054	N
LIST_S2	Benign	0.81	T
MetaRNN	Benign	0.0055	T
PhyloP100		2.0
PrimateAI	Benign	0.29	T
Sift4G	Uncertain	0.044	D
Polyphen		1.0	D
Vest4		0.12
GERP RS		2.4
Varity_R		0.11
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10414398; hg19: chr19-45021210; COSMIC: COSV57601121;