7-100717894-A-G

Variant names:

• chr7-100717894-A-G
• rs1734907

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 0.844 in 152,180 control chromosomes in the GnomAD database, including 54,298 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 0.84 (54298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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: 0.844 AC: 128353 AN: 152062 Hom.: 54259 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.844 AC: 128449 AN: 152180 Hom.: 54298 Cov.: 32 AF XY: 0.843 AC XY: 62719 AN XY: 74382

African (AFR) AF: 0.833 AC: 34586 AN: 41524

American (AMR) AF: 0.893 AC: 13652 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3472

East Asian (EAS) AF: 0.935 AC: 4845 AN: 5184

South Asian (SAS) AF: 0.780 AC: 3766 AN: 4830

European-Finnish (FIN) AF: 0.793 AC: 8371 AN: 10556

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57318 AN: 68020

Other (OTH) AF: 0.859 AC: 1808 AN: 2106

Alfa AF: 0.848 Hom.: 228057

Bravo AF: 0.853

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.65
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1734907; hg19: chr7-100315517;