6-159433591-C-T

Variant names:

• chr6-159433591-C-T
• rs7758822
• ENST00000753126.1:n.201+2891G>A

Variant summary

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

The ENST00000753126.1(ENSG00000231178):​n.201+2891G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,188 control chromosomes in the GnomAD database, including 2,379 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 0.16 (2379 hom., cov: 33)
• Consequence: ENSG00000231178 ENST00000753126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 5 publications found

Genes affected

ENSG00000231178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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
ENSG00000231178	ENST00000753126.1	n.201+2891G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24073 AN: 152070 Hom.: 2380 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.158 AC: 24071 AN: 152188 Hom.: 2379 Cov.: 33 AF XY: 0.165 AC XY: 12248 AN XY: 74386

African (AFR) AF: 0.132 AC: 5471 AN: 41526

American (AMR) AF: 0.134 AC: 2046 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2527 AN: 5164

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1496 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9723 AN: 68006

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.147 Hom.: 2119

Bravo AF: 0.154

Asia WGS AF: 0.396 AC: 1377 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	6.1
DANN	Benign	0.80
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7758822; hg19: chr6-159854623;