rs4256646

Variant names:

• chr9-73182919-G-A
• rs4256646

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 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,089 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 0.50 (19089 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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: 0.501 AC: 76046 AN: 151854 Hom.: 19093 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.500 AC: 76060 AN: 151972 Hom.: 19089 Cov.: 33 AF XY: 0.500 AC XY: 37132 AN XY: 74274

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.516

Alfa AF: 0.515 Hom.: 27635

Bravo AF: 0.496

Asia WGS AF: 0.492 AC: 1704 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4256646; hg19: chr9-75797835;