rs3130237

chr6-33129784-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 0.131 in 152,240 control chromosomes in the GnomAD database, including 1,473 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 0.13 (1473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.131 AC: 19861 AN: 152122 Hom.: 1477 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.131 AC: 19871 AN: 152240 Hom.: 1473 Cov.: 32 AF XY: 0.130 AC XY: 9644 AN XY: 74434

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.116

Alfa AF: 0.155 Hom.: 1766

Bravo AF: 0.120

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.57
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130237; hg19: chr6-33097561;