8-141096129-G-A

Variant names:

• chr8-141096129-G-A
• rs11167023
• ENST00000824422.1:n.140-4705G>A

Variant summary

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

The ENST00000824422.1(ENSG00000307178):​n.140-4705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,888 control chromosomes in the GnomAD database, including 5,056 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 0.25 (5056 hom., cov: 32)
• Consequence: ENSG00000307178 ENST00000824422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 6 publications found

Genes affected

ENSG00000307178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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
ENSG00000307178	ENST00000824422.1	n.140-4705G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37265 AN: 151774 Hom.: 5048 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.245 AC: 37286 AN: 151888 Hom.: 5056 Cov.: 32 AF XY: 0.249 AC XY: 18473 AN XY: 74240

African (AFR) AF: 0.328 AC: 13579 AN: 41388

American (AMR) AF: 0.273 AC: 4174 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.389 AC: 1995 AN: 5126

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12561 AN: 67916

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.202 Hom.: 15408

Bravo AF: 0.247

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs11167023; hg19: chr8-142106228;