19-41559909-G-A

Variant names:

• chr19-41559909-G-A
• rs4803480
• NM_001288773.3:c.-778-4773G>A

Variant summary

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

The NM_001288773.3(CEACAM21):​c.-778-4773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,160 control chromosomes in the GnomAD database, including 2,597 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 0.18 (2597 hom., cov: 32)
• Consequence: CEACAM21 NM_001288773.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 21 publications found

Genes affected

CEACAM21 (HGNC:28834): (CEA cell adhesion molecule 21) 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 (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001288773.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM21	NM_001288773.3		c.-778-4773G>A		intron	N/A	NP_001275702.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM21	ENST00000407170.6	TSL:2	c.-778-4773G>A		intron	N/A	ENSP00000384380.1
	CEACAM21	ENST00000618577.4	TSL:5	n.36-4773G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27806 AN: 152042 Hom.: 2596 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27823 AN: 152160 Hom.: 2597 Cov.: 32 AF XY: 0.182 AC XY: 13519 AN XY: 74382

African (AFR) AF: 0.191 AC: 7907 AN: 41498

American (AMR) AF: 0.152 AC: 2328 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.0597 AC: 310 AN: 5190

South Asian (SAS) AF: 0.171 AC: 823 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2128 AN: 10586

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12970 AN: 67990

Other (OTH) AF: 0.194 AC: 411 AN: 2116

Alfa AF: 0.185 Hom.: 8190

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4803480; hg19: chr19-42066279;