rs10868677

Positions:

• chr9-87996957-C-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 0.401 in 152,074 control chromosomes in the GnomAD database, including 13,123 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 0.40 (13123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

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 (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.401 AC: 60911 AN: 151956 Hom.: 13120 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.401 AC: 60924 AN: 152074 Hom.: 13123 Cov.: 32 AF XY: 0.398 AC XY: 29561 AN XY: 74324

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.404

Alfa AF: 0.469 Hom.: 21608

Bravo AF: 0.385

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10868677; hg19: chr9-90611872;