chr18-7547609-A-G

Variant names:

• chr18-7547609-A-G
• rs982723
• ENST00000839922.1:n.167+20231T>C

Variant summary

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

The ENST00000839922.1(ENSG00000309267):​n.167+20231T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.062 in 151,846 control chromosomes in the GnomAD database, including 410 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 0.062 (410 hom., cov: 32)
• Consequence: ENSG00000309267 ENST00000839922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 1 publications found

Genes affected

ENSG00000309267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 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
ENSG00000309267	ENST00000839922.1	n.167+20231T>C		intron_variant	Intron 1 of 1
ENSG00000309267	ENST00000839923.1	n.133-17467T>C		intron_variant	Intron 1 of 2
ENSG00000309267	ENST00000839924.1	n.108-17437T>C		intron_variant	Intron 1 of 2
ENSG00000309267	ENST00000839925.1	n.108+10613T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9405 AN: 151728 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0620 AC: 9414 AN: 151846 Hom.: 410 Cov.: 32 AF XY: 0.0648 AC XY: 4808 AN XY: 74222

African (AFR) AF: 0.0940 AC: 3892 AN: 41410

American (AMR) AF: 0.0417 AC: 636 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3466

East Asian (EAS) AF: 0.0824 AC: 423 AN: 5136

South Asian (SAS) AF: 0.201 AC: 965 AN: 4800

European-Finnish (FIN) AF: 0.0378 AC: 397 AN: 10510

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2729 AN: 67972

Other (OTH) AF: 0.0620 AC: 130 AN: 2098

Alfa AF: 0.0480 Hom.: 370

Bravo AF: 0.0597

Asia WGS AF: 0.141 AC: 491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.50
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs982723; hg19: chr18-7547607;