chr6-113406128-C-T

Position:

• chr6-113406128-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 0.128 in 152,090 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.128 AC: 19383 AN: 151972 Hom.: 1482 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.128 AC: 19399 AN: 152090 Hom.: 1484 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74370

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.109

Alfa AF: 0.115 Hom.: 201

Bravo AF: 0.126

Asia WGS AF: 0.0830 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484461; hg19: chr6-113727330;