rs10234070

Variant names:

• chr7-44498097-C-T
• rs10234070

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 0.0765 in 152,248 control chromosomes in the GnomAD database, including 615 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 0.076 (615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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: 0.0766 AC: 11652 AN: 152130 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0765 AC: 11644 AN: 152248 Hom.: 615 Cov.: 32 AF XY: 0.0752 AC XY: 5598 AN XY: 74442

African (AFR) AF: 0.0188 AC: 781 AN: 41550

American (AMR) AF: 0.0496 AC: 758 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5194

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4828

European-Finnish (FIN) AF: 0.137 AC: 1453 AN: 10584

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8034 AN: 68014

Other (OTH) AF: 0.0630 AC: 133 AN: 2112

Alfa AF: 0.0992 Hom.: 445

Bravo AF: 0.0658

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.52
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10234070; hg19: chr7-44537696;