ENST00000826972.1:n.203+5959G>A

Variant names:

• chr1-23533029-G-A
• rs6667575
• ENST00000826972.1:n.203+5959G>A

Variant summary

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

The ENST00000826972.1(ENSG00000307540):​n.203+5959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,012 control chromosomes in the GnomAD database, including 5,089 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 0.23 (5089 hom., cov: 32)
• Consequence: ENSG00000307540 ENST00000826972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24
• Publications: 13 publications found

Genes affected

ENSG00000307540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 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
ENSG00000307540	ENST00000826972.1	n.203+5959G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34703 AN: 151894 Hom.: 5097 Cov.: 32

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.228 AC: 34687 AN: 152012 Hom.: 5089 Cov.: 32 AF XY: 0.233 AC XY: 17307 AN XY: 74290

African (AFR) AF: 0.0606 AC: 2515 AN: 41500

American (AMR) AF: 0.281 AC: 4287 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3157 AN: 5166

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2883 AN: 10564

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18144 AN: 67940

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.267 Hom.: 9241

Bravo AF: 0.228

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0020
DANN	Benign	0.69
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs6667575; hg19: chr1-23859521;