rs2670135

Variant names:

• chr6-52687617-A-G
• rs2670135

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 0.539 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 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: 0.539 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

African (AFR) AF: 0.456 AC: 18896 AN: 41460

American (AMR) AF: 0.450 AC: 6870 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3320 AN: 5186

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4818

European-Finnish (FIN) AF: 0.590 AC: 6230 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40664 AN: 67976

Other (OTH) AF: 0.530 AC: 1121 AN: 2114

Alfa AF: 0.559 Hom.: 3593

Bravo AF: 0.522

Asia WGS AF: 0.557 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.45
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs2670135; hg19: chr6-52552415;