rs719673

chr9-4957650-G-Achr9-4957650-G-Cchr9-4957650-G-T

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 0.477 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.478

Alfa AF: 0.518 Hom.: 11722

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719673; hg19: chr9-4957650;