6-67471879-T-C

Position:

• chr6-67471879-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 0.453 in 151,990 control chromosomes in the GnomAD database, including 16,357 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 0.45 (16357 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

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 = 0.593 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: 0.453 AC: 68756 AN: 151872 Hom.: 16346 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.453 AC: 68809 AN: 151990 Hom.: 16357 Cov.: 33 AF XY: 0.448 AC XY: 33279 AN XY: 74286

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.446

Alfa AF: 0.434 Hom.: 2337

Bravo AF: 0.462

Asia WGS AF: 0.309 AC: 1078 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	0.47
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4710655; hg19: chr6-68181772; COSMIC: COSV72736802;