9-136968181-G-A

Variant names:

• chr9-136968181-G-A
• rs57024841
• ENST00000745587.1:n.137-7162C>T

Variant summary

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

The ENST00000745587.1(ENSG00000297111):​n.137-7162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,026 control chromosomes in the GnomAD database, including 19,179 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 0.48 (19179 hom., cov: 32)
• Consequence: ENSG00000297111 ENST00000745587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 12 publications found

Genes affected

ENSG00000297111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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
ENSG00000297111	ENST00000745587.1	n.137-7162C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73243 AN: 151914 Hom.: 19185 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.482 AC: 73260 AN: 152026 Hom.: 19179 Cov.: 32 AF XY: 0.484 AC XY: 35980 AN XY: 74330

African (AFR) AF: 0.296 AC: 12282 AN: 41466

American (AMR) AF: 0.577 AC: 8817 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1952 AN: 3468

East Asian (EAS) AF: 0.175 AC: 903 AN: 5172

South Asian (SAS) AF: 0.439 AC: 2121 AN: 4826

European-Finnish (FIN) AF: 0.612 AC: 6470 AN: 10576

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39006 AN: 67926

Other (OTH) AF: 0.489 AC: 1032 AN: 2112

Alfa AF: 0.517 Hom.: 2536

Bravo AF: 0.471

Asia WGS AF: 0.317 AC: 1103 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs57024841; hg19: chr9-139862633;