chr6-159640058-C-T

Variant names:

• chr6-159640058-C-T
• rs7754103
• ENST00000656085.1:n.42+22528G>A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+22528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,206 control chromosomes in the GnomAD database, including 570 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 0.078 (570 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 7 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=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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.42+22528G>A		intron_variant	Intron 1 of 1
ENSG00000286533	ENST00000794978.1	n.185+22425G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11921 AN: 152088 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0784 AC: 11932 AN: 152206 Hom.: 570 Cov.: 32 AF XY: 0.0785 AC XY: 5840 AN XY: 74408

African (AFR) AF: 0.130 AC: 5398 AN: 41528

American (AMR) AF: 0.0583 AC: 891 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3470

East Asian (EAS) AF: 0.102 AC: 523 AN: 5152

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4818

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0561 AC: 3817 AN: 68014

Other (OTH) AF: 0.0699 AC: 148 AN: 2116

Alfa AF: 0.0695 Hom.: 243

Bravo AF: 0.0812

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7754103; hg19: chr6-160061090;