chr8-141094845-A-G

Variant names:

• chr8-141094845-A-G
• rs4961252
• ENST00000824422.1:n.140-5989A>G

Variant summary

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

The ENST00000824422.1(ENSG00000307178):​n.140-5989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,900 control chromosomes in the GnomAD database, including 21,224 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 0.51 (21224 hom., cov: 31)
• Consequence: ENSG00000307178 ENST00000824422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 23 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824422.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307178	ENST00000824422.1		n.140-5989A>G		intron	N/A
	ENSG00000307200	ENST00000824505.1		n.146+614T>C		intron	N/A
	ENSG00000307200	ENST00000824506.1		n.90+614T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77416 AN: 151784 Hom.: 21209 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.510 AC: 77477 AN: 151900 Hom.: 21224 Cov.: 31 AF XY: 0.515 AC XY: 38204 AN XY: 74232

African (AFR) AF: 0.705 AC: 29167 AN: 41392

American (AMR) AF: 0.472 AC: 7214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3489 AN: 5158

South Asian (SAS) AF: 0.536 AC: 2581 AN: 4812

European-Finnish (FIN) AF: 0.484 AC: 5097 AN: 10524

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27227 AN: 67958

Other (OTH) AF: 0.488 AC: 1028 AN: 2108

Alfa AF: 0.437 Hom.: 63099

Bravo AF: 0.515

Asia WGS AF: 0.600 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4961252; hg19: chr8-142104944;