6-30371825-T-C

Position:

• chr6-30371825-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 0.693 in 151,926 control chromosomes in the GnomAD database, including 36,914 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 0.69 (36914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.693 AC: 105127 AN: 151808 Hom.: 36880 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.693 AC: 105214 AN: 151926 Hom.: 36914 Cov.: 32 AF XY: 0.693 AC XY: 51444 AN XY: 74282

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.658

Alfa AF: 0.652 Hom.: 49846

Bravo AF: 0.693

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844746; hg19: chr6-30339602;