rs2670135

Variant names:

• chr6-52687617-A-G
• rs2670135

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 0.539 in 152,064 control chromosomes in the GnomAD database, including 22,541 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 0.54 (22541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 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: 0.539 AC: 81920 AN: 151946 Hom.: 22516 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.539 AC: 81983 AN: 152064 Hom.: 22541 Cov.: 32 AF XY: 0.538 AC XY: 39967 AN XY: 74352

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.530

Alfa AF: 0.563 Hom.: 3514

Bravo AF: 0.522

Asia WGS AF: 0.557 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
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: rs2670135; hg19: chr6-52552415;