7-62586730-C-T

Variant names:

• chr7-62586730-C-T
• rs2198391

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 0.158 in 151,244 control chromosomes in the GnomAD database, including 2,142 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 0.16 (2142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.158 AC: 23936 AN: 151126 Hom.: 2137 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.158 AC: 23955 AN: 151244 Hom.: 2142 Cov.: 33 AF XY: 0.165 AC XY: 12175 AN XY: 73896

African (AFR) AF: 0.121 AC: 5027 AN: 41398

American (AMR) AF: 0.187 AC: 2820 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 466 AN: 3454

East Asian (EAS) AF: 0.311 AC: 1585 AN: 5090

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4810

European-Finnish (FIN) AF: 0.223 AC: 2350 AN: 10518

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10143 AN: 67594

Other (OTH) AF: 0.161 AC: 336 AN: 2092

Alfa AF: 0.150 Hom.: 3554

Bravo AF: 0.152

Asia WGS AF: 0.264 AC: 916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.61

Splicing

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

Other links and lift over

dbSNP: rs2198391; hg19: chr7-62047108;