6-150541086-G-T

Variant names:

• chr6-150541086-G-T
• rs4311527

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 0.285 in 152,000 control chromosomes in the GnomAD database, including 6,983 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 0.29 (6983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43370 AN: 151882 Hom.: 6977 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.285 AC: 43388 AN: 152000 Hom.: 6983 Cov.: 32 AF XY: 0.294 AC XY: 21868 AN XY: 74268

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.251

Alfa AF: 0.247 Hom.: 1357

Bravo AF: 0.264

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4311527; hg19: chr6-150862222;