rs995967

Variant names:

• chr10-127474105-G-C
• rs995967

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 0.282 in 152,080 control chromosomes in the GnomAD database, including 6,232 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 0.28 (6232 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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: 0.282 AC: 42862 AN: 151962 Hom.: 6225 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0816

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.282 AC: 42892 AN: 152080 Hom.: 6232 Cov.: 33 AF XY: 0.278 AC XY: 20675 AN XY: 74368

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.0816

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.294

Alfa AF: 0.286 Hom.: 780

Bravo AF: 0.278

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs995967; hg19: chr10-129272369;