6-106693420-T-C

Position:

• chr6-106693420-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 0.123 in 152,078 control chromosomes in the GnomAD database, including 1,318 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 0.12 (1318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18678 AN: 151960 Hom.: 1319 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18674 AN: 152078 Hom.: 1318 Cov.: 32 AF XY: 0.123 AC XY: 9120 AN XY: 74334

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0750

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.136

Alfa AF: 0.124 Hom.: 611

Bravo AF: 0.118

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499044; hg19: chr6-107141295;