rs2317314

chr19-41555937-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001288773.3(CEACAM21):c.-779+6385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,070 control chromosomes in the GnomAD database, including 24,850 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 0.57 (24850 hom., cov: 32)
• Consequence: CEACAM21 NM_001288773.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM21	NM_001288773.3	c.-779+6385C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM21	ENST00000407170.6	c.-779+6385C>T		intron_variant		2
CEACAM21	ENST00000618577.4	n.35+6385C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86815 AN: 151950 Hom.: 24817 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.571 AC: 86901 AN: 152070 Hom.: 24850 Cov.: 32 AF XY: 0.571 AC XY: 42473 AN XY: 74346

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.557

Alfa AF: 0.562 Hom.: 6091

Bravo AF: 0.578

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317314; hg19: chr19-42062307;