rs10905718

Variant names:

• chr10-6072893-A-G
• rs10905718

Your query was ambiguous. Multiple possible variants found:

• chr10-6072893-A-G
• chr10-6072893-A-T

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 0.254 in 151,922 control chromosomes in the GnomAD database, including 5,607 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 0.25 (5607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.254 AC: 38576 AN: 151804 Hom.: 5598 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.254 AC: 38598 AN: 151922 Hom.: 5607 Cov.: 32 AF XY: 0.256 AC XY: 19009 AN XY: 74252

African (AFR) AF: 0.131 AC: 5408 AN: 41432

American (AMR) AF: 0.221 AC: 3372 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3460

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3797 AN: 10534

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21478 AN: 67922

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.283 Hom.: 18599

Bravo AF: 0.234

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs10905718; hg19: chr10-6114856;