chr6-25895347-T-C

Position:

• chr6-25895347-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 0.174 in 152,126 control chromosomes in the GnomAD database, including 3,128 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 0.17 (3128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.174 AC: 26482 AN: 152008 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.174 AC: 26497 AN: 152126 Hom.: 3128 Cov.: 31 AF XY: 0.182 AC XY: 13503 AN XY: 74380

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.217

Alfa AF: 0.165 Hom.: 3149

Bravo AF: 0.182

Asia WGS AF: 0.400 AC: 1385 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6910741; hg19: chr6-25895575;