6-6007758-G-C

Position:

• chr6-6007758-G-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 0.401 in 152,110 control chromosomes in the GnomAD database, including 13,665 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 0.40 (13665 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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: 0.401 AC: 60928 AN: 151992 Hom.: 13619 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.401 AC: 61034 AN: 152110 Hom.: 13665 Cov.: 33 AF XY: 0.406 AC XY: 30160 AN XY: 74348

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.378

Alfa AF: 0.206 Hom.: 417

Bravo AF: 0.419

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs582262; hg19: chr6-6007991;