19-35647577-A-C

Variant names:

• chr19-35647577-A-C
• rs6510502

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 0.157 in 149,368 control chromosomes in the GnomAD database, including 2,016 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 0.16 (2016 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 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: 0.157 AC: 23404 AN: 149250 Hom.: 2009 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0624

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0682

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.157 AC: 23444 AN: 149368 Hom.: 2016 Cov.: 30 AF XY: 0.158 AC XY: 11516 AN XY: 72892

African (AFR) AF: 0.213 AC: 8652 AN: 40540

American (AMR) AF: 0.219 AC: 3271 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.0624 AC: 215 AN: 3448

East Asian (EAS) AF: 0.0738 AC: 366 AN: 4960

South Asian (SAS) AF: 0.147 AC: 693 AN: 4712

European-Finnish (FIN) AF: 0.154 AC: 1586 AN: 10276

Middle Eastern (MID) AF: 0.0660 AC: 19 AN: 288

European-Non Finnish (NFE) AF: 0.120 AC: 8096 AN: 67242

Other (OTH) AF: 0.163 AC: 338 AN: 2072

Alfa AF: 0.128 Hom.: 2269

Bravo AF: 0.166

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.26
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs6510502; hg19: chr19-36138479; COSMIC: COSV55837000;