rs3760657

Variant names:

• chr19-40989528-A-G
• rs3760657

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.093 in 152,198 control chromosomes in the GnomAD database, including 880 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.093 (880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 19-40989528-A-G is Benign according to our data. Variant chr19-40989528-A-G is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 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: 0.0930 AC: 14140 AN: 152080 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0930 AC: 14150 AN: 152198 Hom.: 880 Cov.: 32 AF XY: 0.0979 AC XY: 7284 AN XY: 74414

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.0938

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0934 Hom.: 732

Bravo AF: 0.0918

Asia WGS AF: 0.144 AC: 498 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760657; hg19: chr19-41495433;