6-93827537-T-C

Position:

• chr6-93827537-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 0.554 in 151,894 control chromosomes in the GnomAD database, including 23,596 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 0.55 (23596 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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: 0.554 AC: 84053 AN: 151778 Hom.: 23578 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.554 AC: 84122 AN: 151894 Hom.: 23596 Cov.: 32 AF XY: 0.556 AC XY: 41275 AN XY: 74246

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.521

Alfa AF: 0.495 Hom.: 3393

Bravo AF: 0.544

Asia WGS AF: 0.624 AC: 2152 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336071; hg19: chr6-94537255; COSMIC: COSV62494147;