10-2687638-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;