rs1075394

Variant names:

• chr8-100392722-A-G
• rs1075394
• ENST00000519844.2:n.153-10951T>C

Variant summary

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

The ENST00000519844.2(ENSG00000253824):​n.153-10951T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,034 control chromosomes in the GnomAD database, including 23,728 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 0.56 (23728 hom., cov: 32)
• Consequence: ENSG00000253824 ENST00000519844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 1 publications found

Genes affected

ENSG00000253824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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
ENSG00000253824	ENST00000519844.2	n.153-10951T>C		intron_variant	Intron 2 of 2	3
ENSG00000253824	ENST00000523870.2	n.247+2659T>C		intron_variant	Intron 2 of 2	2
ENSG00000253824	ENST00000654832.1	n.181-10951T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84420 AN: 151916 Hom.: 23688 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.556 AC: 84520 AN: 152034 Hom.: 23728 Cov.: 32 AF XY: 0.553 AC XY: 41059 AN XY: 74314

African (AFR) AF: 0.636 AC: 26376 AN: 41476

American (AMR) AF: 0.550 AC: 8408 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3466

East Asian (EAS) AF: 0.419 AC: 2172 AN: 5180

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4814

European-Finnish (FIN) AF: 0.565 AC: 5969 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35835 AN: 67952

Other (OTH) AF: 0.557 AC: 1174 AN: 2106

Alfa AF: 0.535 Hom.: 84251

Bravo AF: 0.559

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.75
PhyloP100		-1.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1075394; hg19: chr8-101404950;