rs3130653

chr6-30854994-C-A

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 0.488 in 151,944 control chromosomes in the GnomAD database, including 19,059 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 0.49 (19059 hom., cov: 31)
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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: 0.488 AC: 74155 AN: 151826 Hom.: 19046 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.488 AC: 74207 AN: 151944 Hom.: 19059 Cov.: 31 AF XY: 0.482 AC XY: 35792 AN XY: 74244

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.469

Alfa AF: 0.568 Hom.: 15390

Bravo AF: 0.476

Asia WGS AF: 0.313 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.60
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130653; hg19: chr6-30822771;