chr7-6370690-A-G

Position:

• chr7-6370690-A-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6370690A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.594

Alfa AF: 0.546 Hom.: 12781

Bravo AF: 0.645

Asia WGS AF: 0.824 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2689420; hg19: chr7-6410321;