7-6372977-G-T

Variant names:

• chr7-6372977-G-T
• rs1647224

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 0.131 in 151,624 control chromosomes in the GnomAD database, including 2,528 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 0.13 (2528 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.131 AC: 19855 AN: 151506 Hom.: 2506 Cov.: 29

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.131 AC: 19915 AN: 151624 Hom.: 2528 Cov.: 29 AF XY: 0.141 AC XY: 10482 AN XY: 74084

African (AFR) AF: 0.234 AC: 9668 AN: 41304

American (AMR) AF: 0.169 AC: 2574 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3466

East Asian (EAS) AF: 0.558 AC: 2854 AN: 5116

South Asian (SAS) AF: 0.280 AC: 1342 AN: 4790

European-Finnish (FIN) AF: 0.0930 AC: 978 AN: 10514

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1922 AN: 67936

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.0753 Hom.: 117

Bravo AF: 0.136

Asia WGS AF: 0.430 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1647224; hg19: chr7-6412608;