rs995967

Variant names:

• chr10-127474105-G-C
• rs995967

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 0.282 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.282 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

African (AFR) AF: 0.275 AC: 11410 AN: 41474

American (AMR) AF: 0.227 AC: 3466 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3472

East Asian (EAS) AF: 0.0816 AC: 422 AN: 5172

South Asian (SAS) AF: 0.289 AC: 1396 AN: 4824

European-Finnish (FIN) AF: 0.289 AC: 3055 AN: 10568

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20921 AN: 67972

Other (OTH) AF: 0.294 AC: 619 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs995967; hg19: chr10-129272369;