chr7-6370690-A-G

Variant names:

• chr7-6370690-A-G
• rs2689420

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 0.633 in 152,026 control chromosomes in the GnomAD database, including 32,372 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 0.63 (32372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.633 AC: 96086 AN: 151908 Hom.: 32304 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.633 AC: 96214 AN: 152026 Hom.: 32372 Cov.: 32 AF XY: 0.641 AC XY: 47619 AN XY: 74328

African (AFR) AF: 0.843 AC: 34970 AN: 41504

American (AMR) AF: 0.657 AC: 10006 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1347 AN: 3464

East Asian (EAS) AF: 0.913 AC: 4726 AN: 5176

South Asian (SAS) AF: 0.655 AC: 3152 AN: 4814

European-Finnish (FIN) AF: 0.609 AC: 6438 AN: 10576

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33768 AN: 67948

Other (OTH) AF: 0.594 AC: 1253 AN: 2108

Alfa AF: 0.557 Hom.: 51976

Bravo AF: 0.645

Asia WGS AF: 0.824 AC: 2862 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	0.29
DANN	Benign	0.45
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2689420; hg19: chr7-6410321;