6-36660265-T-G

Position:

• chr6-36660265-T-G

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 152,110 control chromosomes in the GnomAD database, including 24,704 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 (24704 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36660265T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84173 AN: 151992 Hom.: 24654 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.554 AC: 84286 AN: 152110 Hom.: 24704 Cov.: 32 AF XY: 0.551 AC XY: 40994 AN XY: 74354

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.571

Alfa AF: 0.471 Hom.: 23010

Bravo AF: 0.577

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9462209; hg19: chr6-36628042;