6-120864232-T-C

Position:

• chr6-120864232-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 0.44 in 151,410 control chromosomes in the GnomAD database, including 17,384 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 0.44 (17384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.440 AC: 66573 AN: 151290 Hom.: 17335 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.440 AC: 66687 AN: 151410 Hom.: 17384 Cov.: 32 AF XY: 0.441 AC XY: 32673 AN XY: 74038

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.436

Alfa AF: 0.377 Hom.: 1561

Bravo AF: 0.477

Asia WGS AF: 0.586 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817957; hg19: chr6-121185378;