6-159523964-C-T

Variant names:

• chr6-159523964-C-T
• rs409359
• ENST00000656085.1:n.43-54449G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656085.1(ENSG00000286533):​n.43-54449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,958 control chromosomes in the GnomAD database, including 17,108 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 0.46 (17108 hom., cov: 31)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 6 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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
ENSG00000286533	ENST00000656085.1	n.43-54449G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70229 AN: 151840 Hom.: 17097 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.462 AC: 70273 AN: 151958 Hom.: 17108 Cov.: 31 AF XY: 0.468 AC XY: 34767 AN XY: 74282

African (AFR) AF: 0.291 AC: 12048 AN: 41424

American (AMR) AF: 0.495 AC: 7570 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1855 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3400 AN: 5164

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4818

European-Finnish (FIN) AF: 0.570 AC: 6010 AN: 10540

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 34968 AN: 67960

Other (OTH) AF: 0.480 AC: 1007 AN: 2100

Alfa AF: 0.506 Hom.: 78258

Bravo AF: 0.447

Asia WGS AF: 0.628 AC: 2184 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs409359; hg19: chr6-159944996;