rs10817678

Positions:

• chr9-114817177-G-A

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 0.735 in 152,088 control chromosomes in the GnomAD database, including 42,033 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 0.74 (42033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 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: 0.735 AC: 111736 AN: 151970 Hom.: 41981 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.735 AC: 111850 AN: 152088 Hom.: 42033 Cov.: 32 AF XY: 0.735 AC XY: 54632 AN XY: 74338

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.715

Alfa AF: 0.731 Hom.: 5910

Bravo AF: 0.743

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817678; hg19: chr9-117579457;