chr6-47344162-T-C

Position:

• chr6-47344162-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 0.104 in 152,202 control chromosomes in the GnomAD database, including 1,827 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 0.10 (1827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.104 AC: 15780 AN: 152084 Hom.: 1819 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.104 AC: 15810 AN: 152202 Hom.: 1827 Cov.: 32 AF XY: 0.111 AC XY: 8270 AN XY: 74416

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0584

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0706 Hom.: 999

Bravo AF: 0.117

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10948347; hg19: chr6-47311898;