chr19-44548749-A-G

Variant names:

• chr19-44548749-A-G
• rs1661167
• ENST00000446628.5:n.498+149T>C

Variant summary

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

The ENST00000446628.5(CEACAM22P):​n.498+149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,280 control chromosomes in the GnomAD database, including 1,148 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1144 hom., cov: 32)
  • Exomes 𝑓: 0.21 (4 hom.)
• Consequence: CEACAM22P ENST00000446628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 6 publications found

Genes affected

CEACAM22P (HGNC:):

CEACAM22P (HGNC:38029): (CEA cell adhesion molecule 22, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446628.5. 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
	CEACAM22P	NR_027754.2		n.498+149T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM22P	ENST00000446628.5	TSL:2	n.498+149T>C		intron	N/A
	CEACAM22P	ENST00000455058.1	TSL:6	n.269+149T>C		intron	N/A
	CEACAM22P	ENST00000455455.1	TSL:4	n.424+149T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18460 AN: 152094 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.206 AC: 14 AN: 68 Hom.: 4 AF XY: 0.295 AC XY: 13 AN XY: 44

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.155 AC: 9 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.121 AC: 18453 AN: 152212 Hom.: 1144 Cov.: 32 AF XY: 0.123 AC XY: 9123 AN XY: 74400

African (AFR) AF: 0.107 AC: 4439 AN: 41530

American (AMR) AF: 0.0951 AC: 1454 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.154 AC: 796 AN: 5182

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1404 AN: 10596

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8504 AN: 68002

Other (OTH) AF: 0.129 AC: 274 AN: 2116

Alfa AF: 0.124 Hom.: 2204

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
PhyloP100		0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1661167;

hg19: chr19-45052068;