6-147480836-C-T

Variant names:

• chr6-147480836-C-T
• rs325109

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 0.605 in 151,216 control chromosomes in the GnomAD database, including 29,469 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 0.61 (29469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.605 AC: 91469 AN: 151098 Hom.: 29453 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.605 AC: 91537 AN: 151216 Hom.: 29469 Cov.: 31 AF XY: 0.603 AC XY: 44531 AN XY: 73872

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.633

Alfa AF: 0.642 Hom.: 3497

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325109; hg19: chr6-147801972;