rs3810253

Variant names:

• chr19-14476257-A-C
• rs3810253

Your query was ambiguous. Multiple possible variants found:

• chr19-14476257-A-C
• chr19-14476257-A-T

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 0.345 in 151,204 control chromosomes in the GnomAD database, including 11,611 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 0.34 (11611 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.344 AC: 52036 AN: 151086 Hom.: 11565 Cov.: 29

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.345 AC: 52138 AN: 151204 Hom.: 11611 Cov.: 29 AF XY: 0.348 AC XY: 25668 AN XY: 73812

African (AFR) AF: 0.585 AC: 24095 AN: 41208

American (AMR) AF: 0.354 AC: 5381 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3697 AN: 5082

South Asian (SAS) AF: 0.346 AC: 1644 AN: 4758

European-Finnish (FIN) AF: 0.202 AC: 2116 AN: 10456

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13415 AN: 67732

Other (OTH) AF: 0.326 AC: 684 AN: 2098

Alfa AF: 0.253 Hom.: 14147

Bravo AF: 0.369

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs3810253; hg19: chr19-14587069;