7-106369275-C-T

Variant names:

• chr7-106369275-C-T
• rs179863

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 0.603 in 151,666 control chromosomes in the GnomAD database, including 28,912 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 0.60 (28912 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.603 AC: 91359 AN: 151548 Hom.: 28883 Cov.: 28

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.603 AC: 91448 AN: 151666 Hom.: 28912 Cov.: 28 AF XY: 0.601 AC XY: 44501 AN XY: 74076

African (AFR) AF: 0.786 AC: 32499 AN: 41354

American (AMR) AF: 0.619 AC: 9425 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4046 AN: 5138

South Asian (SAS) AF: 0.661 AC: 3169 AN: 4794

European-Finnish (FIN) AF: 0.460 AC: 4826 AN: 10492

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33803 AN: 67878

Other (OTH) AF: 0.605 AC: 1271 AN: 2100

Alfa AF: 0.542 Hom.: 12991

Bravo AF: 0.625

Asia WGS AF: 0.678 AC: 2357 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	7.1
DANN	Benign	0.65
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs179863; hg19: chr7-106009721;