rs719673

Variant names:

• chr9-4957650-G-A
• rs719673

Your query was ambiguous. Multiple possible variants found:

• chr9-4957650-G-A
• chr9-4957650-G-C
• chr9-4957650-G-T

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 0.477 in 151,834 control chromosomes in the GnomAD database, including 18,952 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 0.48 (18952 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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: 0.478 AC: 72446 AN: 151716 Hom.: 18947 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.477 AC: 72471 AN: 151834 Hom.: 18952 Cov.: 31 AF XY: 0.483 AC XY: 35831 AN XY: 74194

African (AFR) AF: 0.246 AC: 10193 AN: 41406

American (AMR) AF: 0.507 AC: 7738 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3468

East Asian (EAS) AF: 0.760 AC: 3937 AN: 5178

South Asian (SAS) AF: 0.567 AC: 2726 AN: 4812

European-Finnish (FIN) AF: 0.588 AC: 6170 AN: 10492

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38396 AN: 67906

Other (OTH) AF: 0.478 AC: 1008 AN: 2110

Alfa AF: 0.523 Hom.: 19635

Bravo AF: 0.459

Asia WGS AF: 0.611 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.2
DANN	Benign	0.91
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs719673; hg19: chr9-4957650;