10-2687638-C-G

Variant names:

• chr10-2687638-C-G
• rs7097880

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 0.35 in 151,942 control chromosomes in the GnomAD database, including 9,834 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 0.35 (9834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53221 AN: 151824 Hom.: 9830 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.350 AC: 53244 AN: 151942 Hom.: 9834 Cov.: 32 AF XY: 0.362 AC XY: 26854 AN XY: 74266

African (AFR) AF: 0.247 AC: 10212 AN: 41414

American (AMR) AF: 0.435 AC: 6650 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2124 AN: 5164

South Asian (SAS) AF: 0.424 AC: 2038 AN: 4810

European-Finnish (FIN) AF: 0.527 AC: 5557 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24213 AN: 67940

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.359 Hom.: 1256

Bravo AF: 0.337

Asia WGS AF: 0.438 AC: 1523 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.59
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7097880; hg19: chr10-2729830;