6-30963282-C-T

Position:

• chr6-30963282-C-T

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 0.0485 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0287

Gnomad4 ASJ AF: 0.0400

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0221

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0190 Hom.: 15

Bravo AF: 0.0492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6928738; hg19: chr6-30931059;