rs10868677

Variant names:

• chr9-87996957-C-T
• rs10868677

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.267 AC: 11096 AN: 41506

American (AMR) AF: 0.365 AC: 5569 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1053 AN: 5180

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4406 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33120 AN: 67958

Other (OTH) AF: 0.404 AC: 854 AN: 2116

Alfa AF: 0.468 Hom.: 25304

Bravo AF: 0.385

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.83
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10868677; hg19: chr9-90611872;