chr10-67863513-A-G

Variant names:

• chr10-67863513-A-G
• rs17712705

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 0.651 in 151,868 control chromosomes in the GnomAD database, including 33,299 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 0.65 (33299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98871 AN: 151750 Hom.: 33278 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.651 AC: 98934 AN: 151868 Hom.: 33299 Cov.: 31 AF XY: 0.641 AC XY: 47528 AN XY: 74196

African (AFR) AF: 0.732 AC: 30311 AN: 41430

American (AMR) AF: 0.581 AC: 8845 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3468

East Asian (EAS) AF: 0.150 AC: 776 AN: 5158

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6177 AN: 10480

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46166 AN: 67976

Other (OTH) AF: 0.649 AC: 1365 AN: 2102

Alfa AF: 0.658 Hom.: 25123

Bravo AF: 0.652

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs17712705; hg19: chr10-69623271;