chr3-39730960-A-G

Variant names:

• chr3-39730960-A-G
• rs1527566

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 0.364 in 151,984 control chromosomes in the GnomAD database, including 12,842 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 0.36 (12842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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: 0.363 AC: 55187 AN: 151866 Hom.: 12794 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.364 AC: 55284 AN: 151984 Hom.: 12842 Cov.: 31 AF XY: 0.358 AC XY: 26615 AN XY: 74282

African (AFR) AF: 0.672 AC: 27853 AN: 41424

American (AMR) AF: 0.262 AC: 4003 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5158

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2166 AN: 10576

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17056 AN: 67962

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.282 Hom.: 3717

Bravo AF: 0.378

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.25
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1527566; hg19: chr3-39772451;