rs656319

chr8-9956901-A-Gchr8-9956901-A-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 0.489 in 152,004 control chromosomes in the GnomAD database, including 18,963 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 0.49 (18963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 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: 0.489 AC: 74254 AN: 151886 Hom.: 18954 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.489 AC: 74299 AN: 152004 Hom.: 18963 Cov.: 32 AF XY: 0.478 AC XY: 35542 AN XY: 74318

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.523

Alfa AF: 0.531 Hom.: 10901

Bravo AF: 0.486

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs656319; hg19: chr8-9814411;