6-30963282-C-T

Variant names:

• chr6-30963282-C-T
• rs6928738

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 0.0485 in 139,252 control chromosomes in the GnomAD database, including 281 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 0.049 (281 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 6753 AN: 139140 Hom.: 280 Cov.: 29

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00977

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0489

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0523

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

GnomAD4 genome AF: 0.0485 AC: 6759 AN: 139252 Hom.: 281 Cov.: 29 AF XY: 0.0483 AC XY: 3287 AN XY: 68028

African (AFR) AF: 0.104 AC: 4164 AN: 39974

American (AMR) AF: 0.0287 AC: 417 AN: 14544

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 119 AN: 2978

East Asian (EAS) AF: 0.0267 AC: 133 AN: 4988

South Asian (SAS) AF: 0.0940 AC: 381 AN: 4054

European-Finnish (FIN) AF: 0.0104 AC: 99 AN: 9542

Middle Eastern (MID) AF: 0.0403 AC: 10 AN: 248

European-Non Finnish (NFE) AF: 0.0221 AC: 1331 AN: 60358

Other (OTH) AF: 0.0507 AC: 99 AN: 1952

Alfa AF: 0.0275 Hom.: 174

Bravo AF: 0.0492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.75
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6928738; hg19: chr6-30931059;