chr19-57349717-T-C

Variant names:

• chr19-57349717-T-C
• rs7250371

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 0.64 in 152,086 control chromosomes in the GnomAD database, including 31,521 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 0.64 (31521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.640 AC: 97299 AN: 151968 Hom.: 31478 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.640 AC: 97386 AN: 152086 Hom.: 31521 Cov.: 32 AF XY: 0.639 AC XY: 47541 AN XY: 74342

African (AFR) AF: 0.687 AC: 28509 AN: 41476

American (AMR) AF: 0.636 AC: 9714 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1912 AN: 3462

East Asian (EAS) AF: 0.490 AC: 2541 AN: 5182

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4818

European-Finnish (FIN) AF: 0.700 AC: 7399 AN: 10570

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.635 AC: 43188 AN: 67996

Other (OTH) AF: 0.600 AC: 1267 AN: 2110

Alfa AF: 0.628 Hom.: 19048

Bravo AF: 0.640

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7250371; hg19: chr19-57861085;