6-159529503-A-G

Position:

• chr6-159529503-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656085.1(ENSG00000286533):​n.43-59988T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,084 control chromosomes in the GnomAD database, including 12,049 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 0.38 (12049 hom., cov: 33)
• Consequence: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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
	ENST00000656085.1	n.43-59988T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57254 AN: 151966 Hom.: 12019 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.377 AC: 57335 AN: 152084 Hom.: 12049 Cov.: 33 AF XY: 0.385 AC XY: 28584 AN XY: 74314

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.389

Alfa AF: 0.300 Hom.: 1527

Bravo AF: 0.390

Asia WGS AF: 0.632 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs382440; hg19: chr6-159950535;