rs2395670

Variant names:

• chr6-37115033-A-G
• rs2395670

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 0.694 in 151,950 control chromosomes in the GnomAD database, including 36,839 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 0.69 (36839 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105335 AN: 151832 Hom.: 36788 Cov.: 30

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.694 AC: 105451 AN: 151950 Hom.: 36839 Cov.: 30 AF XY: 0.696 AC XY: 51642 AN XY: 74242

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.724

Alfa AF: 0.679 Hom.: 72867

Bravo AF: 0.701

Asia WGS AF: 0.796 AC: 2772 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	3.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395670; hg19: chr6-37082809;