6-30929245-T-C

Variant names:

• chr6-30929245-T-C
• rs2517459

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 0.745 in 152,090 control chromosomes in the GnomAD database, including 42,677 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 0.74 (42677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 30 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 = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113192 AN: 151972 Hom.: 42633 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.745 AC: 113285 AN: 152090 Hom.: 42677 Cov.: 32 AF XY: 0.749 AC XY: 55722 AN XY: 74374

African (AFR) AF: 0.631 AC: 26161 AN: 41442

American (AMR) AF: 0.773 AC: 11823 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3081 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4852 AN: 5178

South Asian (SAS) AF: 0.903 AC: 4353 AN: 4822

European-Finnish (FIN) AF: 0.791 AC: 8375 AN: 10586

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52120 AN: 67990

Other (OTH) AF: 0.728 AC: 1534 AN: 2108

Alfa AF: 0.765 Hom.: 120350

Bravo AF: 0.738

Asia WGS AF: 0.886 AC: 3081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs2517459; hg19: chr6-30897022;