rs3135034

Variant names:

• chr6-32983885-T-C
• rs3135034

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 0.0575 in 152,302 control chromosomes in the GnomAD database, including 313 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 0.058 (313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0919 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: 0.0576 AC: 8763 AN: 152184 Hom.: 313 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0575 AC: 8764 AN: 152302 Hom.: 313 Cov.: 32 AF XY: 0.0565 AC XY: 4210 AN XY: 74476

African (AFR) AF: 0.0166 AC: 692 AN: 41566

American (AMR) AF: 0.0457 AC: 699 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3472

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5188

South Asian (SAS) AF: 0.0992 AC: 479 AN: 4828

European-Finnish (FIN) AF: 0.0606 AC: 643 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0814 AC: 5540 AN: 68018

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0725 Hom.: 1456

Bravo AF: 0.0554

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3135034; hg19: chr6-32951662;