chr2-14431620-T-C

Variant names:

• chr2-14431620-T-C
• rs4145975

Variant summary

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

The variant allele was found at a frequency of 0.49 in 151,878 control chromosomes in the GnomAD database, including 18,669 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 0.49 (18669 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74376 AN: 151760 Hom.: 18647 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.490 AC: 74453 AN: 151878 Hom.: 18669 Cov.: 32 AF XY: 0.488 AC XY: 36220 AN XY: 74230

African (AFR) AF: 0.388 AC: 16079 AN: 41412

American (AMR) AF: 0.475 AC: 7247 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2619 AN: 5146

South Asian (SAS) AF: 0.520 AC: 2504 AN: 4820

European-Finnish (FIN) AF: 0.501 AC: 5262 AN: 10502

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36907 AN: 67948

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.524 Hom.: 11422

Bravo AF: 0.484

Asia WGS AF: 0.497 AC: 1723 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4145975; hg19: chr2-14571744;