8-81507193-G-C

Variant names:

• chr8-81507193-G-C
• rs1843560
• ENST00000524085.2:n.434+9141G>C

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.434+9141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,986 control chromosomes in the GnomAD database, including 12,744 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 0.38 (12744 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 1 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.518-18650G>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.434+9141G>C		intron_variant	Intron 3 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-14514G>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-14514G>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-14514G>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58362 AN: 151868 Hom.: 12698 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.385 AC: 58470 AN: 151986 Hom.: 12744 Cov.: 32 AF XY: 0.382 AC XY: 28395 AN XY: 74312

African (AFR) AF: 0.593 AC: 24556 AN: 41438

American (AMR) AF: 0.403 AC: 6157 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.129 AC: 667 AN: 5184

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2968 AN: 10540

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20223 AN: 67950

Other (OTH) AF: 0.380 AC: 803 AN: 2114

Alfa AF: 0.340 Hom.: 1169

Bravo AF: 0.401

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs1843560; hg19: chr8-82419428;