rs3760657

Positions:

• chr19-40989528-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;