10-62678726-G-C

Variant names:

• chr10-62678726-G-C
• rs10995271

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 0.325 in 152,036 control chromosomes in the GnomAD database, including 8,845 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 0.32 (8845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 66 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.325 AC: 49403 AN: 151918 Hom.: 8848 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.325 AC: 49391 AN: 152036 Hom.: 8845 Cov.: 32 AF XY: 0.325 AC XY: 24168 AN XY: 74326

African (AFR) AF: 0.182 AC: 7547 AN: 41466

American (AMR) AF: 0.252 AC: 3853 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2734 AN: 5176

South Asian (SAS) AF: 0.376 AC: 1813 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4230 AN: 10552

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26598 AN: 67946

Other (OTH) AF: 0.318 AC: 672 AN: 2116

Alfa AF: 0.375 Hom.: 6186

Bravo AF: 0.308

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.72
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10995271; hg19: chr10-64438486;