6-151622504-T-C

Variant names:

• chr6-151622504-T-C
• rs4591859

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 0.504 in 152,036 control chromosomes in the GnomAD database, including 19,596 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 0.50 (19596 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.504 AC: 76520 AN: 151918 Hom.: 19576 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.504 AC: 76579 AN: 152036 Hom.: 19596 Cov.: 31 AF XY: 0.497 AC XY: 36928 AN XY: 74292

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.519

Alfa AF: 0.493 Hom.: 5704

Bravo AF: 0.501

Asia WGS AF: 0.483 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4591859; hg19: chr6-151943639;