chr10-2687638-C-G

Variant names:

• chr10-2687638-C-G
• rs7097880

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 0.35 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.351 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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.338

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7097880; hg19: chr10-2729830;