7-104252564-T-G

Variant names:

• chr7-104252564-T-G
• rs10259086

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 0.469 in 151,904 control chromosomes in the GnomAD database, including 19,278 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 0.47 (19278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.469 AC: 71190 AN: 151786 Hom.: 19231 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.469 AC: 71292 AN: 151904 Hom.: 19278 Cov.: 32 AF XY: 0.472 AC XY: 35011 AN XY: 74250

African (AFR) AF: 0.732 AC: 30348 AN: 41444

American (AMR) AF: 0.543 AC: 8274 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2862 AN: 5134

South Asian (SAS) AF: 0.358 AC: 1722 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10536

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21919 AN: 67944

Other (OTH) AF: 0.444 AC: 936 AN: 2110

Alfa AF: 0.366 Hom.: 46610

Bravo AF: 0.500

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10259086; hg19: chr7-103893012;