rs3135034

chr6-32983885-T-C

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 0.0575 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0814

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0783 Hom.: 630

Bravo AF: 0.0554

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135034; hg19: chr6-32951662;