rs1876381

Variant names:

• chr8-82046088-T-C
• rs1876381
• ENST00000659043.1:n.59+12250T>C

Variant summary

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

The ENST00000659043.1(ENSG00000254394):​n.59+12250T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,332 control chromosomes in the GnomAD database, including 3,099 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 0.20 (3099 hom., cov: 28)
• Consequence: ENSG00000254394 ENST00000659043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 0 publications found

Genes affected

ENSG00000254394 (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 (NFE) allele frequency at 95% confidence interval = 0.209 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
ENSG00000254394	ENST00000659043.1	n.59+12250T>C		intron_variant	Intron 1 of 4
ENSG00000254394	ENST00000663058.1	n.306+12250T>C		intron_variant	Intron 1 of 7
ENSG00000254394	ENST00000848452.1	n.88+12250T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30366 AN: 151214 Hom.: 3097 Cov.: 28

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.201 AC: 30382 AN: 151332 Hom.: 3099 Cov.: 28 AF XY: 0.199 AC XY: 14746 AN XY: 73952

African (AFR) AF: 0.207 AC: 8544 AN: 41192

American (AMR) AF: 0.164 AC: 2496 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 779 AN: 3462

East Asian (EAS) AF: 0.141 AC: 723 AN: 5138

South Asian (SAS) AF: 0.150 AC: 721 AN: 4794

European-Finnish (FIN) AF: 0.209 AC: 2176 AN: 10396

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14356 AN: 67844

Other (OTH) AF: 0.197 AC: 415 AN: 2102

Alfa AF: 0.215 Hom.: 764

Asia WGS AF: 0.137 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs1876381; hg19: chr8-82958323;