chr3-191967038-G-T

Variant names:

• chr3-191967038-G-T
• rs2669973

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 0.662 in 152,052 control chromosomes in the GnomAD database, including 34,146 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 0.66 (34146 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 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: 0.662 AC: 100540 AN: 151934 Hom.: 34128 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.662 AC: 100604 AN: 152052 Hom.: 34146 Cov.: 33 AF XY: 0.662 AC XY: 49197 AN XY: 74314

African (AFR) AF: 0.519 AC: 21505 AN: 41458

American (AMR) AF: 0.644 AC: 9846 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2281 AN: 5160

South Asian (SAS) AF: 0.742 AC: 3586 AN: 4834

European-Finnish (FIN) AF: 0.781 AC: 8242 AN: 10550

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50529 AN: 67980

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.723 Hom.: 58982

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.36
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2669973; hg19: chr3-191684827;