6-6012488-T-C

Position:

• chr6-6012488-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 0.355 in 152,086 control chromosomes in the GnomAD database, including 10,396 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 0.36 (10396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.355 AC: 53994 AN: 151968 Hom.: 10384 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.355 AC: 54032 AN: 152086 Hom.: 10396 Cov.: 32 AF XY: 0.352 AC XY: 26164 AN XY: 74346

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.349

Alfa AF: 0.302 Hom.: 1517

Bravo AF: 0.363

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9405890; hg19: chr6-6012721;