chr7-99960817-C-T

Variant names:

• chr7-99960817-C-T
• rs2107349

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 0.975 in 151,948 control chromosomes in the GnomAD database, including 72,161 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 0.97 (72161 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 6 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 = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.975 AC: 147969 AN: 151830 Hom.: 72105 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.975 AC: 148085 AN: 151948 Hom.: 72161 Cov.: 29 AF XY: 0.975 AC XY: 72417 AN XY: 74254

African (AFR) AF: 0.980 AC: 40616 AN: 41430

American (AMR) AF: 0.968 AC: 14768 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3381 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5139 AN: 5152

South Asian (SAS) AF: 0.966 AC: 4636 AN: 4798

European-Finnish (FIN) AF: 0.984 AC: 10442 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.970 AC: 65885 AN: 67930

Other (OTH) AF: 0.966 AC: 2033 AN: 2104

Alfa AF: 0.970 Hom.: 64839

Bravo AF: 0.974

Asia WGS AF: 0.973 AC: 3385 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	0.36
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2107349; hg19: chr7-99558440;