3-102029794-A-G

Variant names:

• chr3-102029794-A-G
• rs771767

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.705 in 151,938 control chromosomes in the GnomAD database, including 38,215 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 0.70 (38215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.705 AC: 107025 AN: 151822 Hom.: 38201 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.705 AC: 107078 AN: 151938 Hom.: 38215 Cov.: 32 AF XY: 0.709 AC XY: 52674 AN XY: 74306

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.697

Alfa AF: 0.714 Hom.: 67692

Bravo AF: 0.695

Asia WGS AF: 0.831 AC: 2889 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	0.37
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs771767; hg19: chr3-101748638;