rs10868677

Variant names:

• chr9-87996957-C-T
• rs10868677

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;