rs7906704

Variant names:

• chr10-113671481-G-T
• rs7906704

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 0.253 in 152,060 control chromosomes in the GnomAD database, including 5,160 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 (5160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 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: 0.253 AC: 38436 AN: 151942 Hom.: 5158 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.253 AC: 38462 AN: 152060 Hom.: 5160 Cov.: 32 AF XY: 0.253 AC XY: 18823 AN XY: 74344

African (AFR) AF: 0.311 AC: 12893 AN: 41442

American (AMR) AF: 0.183 AC: 2793 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1389 AN: 5156

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2538 AN: 10580

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15267 AN: 67990

Other (OTH) AF: 0.252 AC: 531 AN: 2106

Alfa AF: 0.239 Hom.: 13866

Bravo AF: 0.250

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7906704; hg19: chr10-115431240;