8-42112252-G-A

Variant names:

• chr8-42112252-G-A
• rs7840827
• ENST00000837845.1:n.344+1969G>A

Variant summary

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

The ENST00000837845.1(ENSG00000309019):​n.344+1969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,070 control chromosomes in the GnomAD database, including 9,288 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 0.30 (9288 hom., cov: 32)
• Consequence: ENSG00000309019 ENST00000837845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 0 publications found

Genes affected

ENSG00000309019 (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 = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837845.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309019	ENST00000837845.1		n.344+1969G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45988 AN: 151952 Hom.: 9269 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.303 AC: 46047 AN: 152070 Hom.: 9288 Cov.: 32 AF XY: 0.300 AC XY: 22323 AN XY: 74346

African (AFR) AF: 0.576 AC: 23879 AN: 41456

American (AMR) AF: 0.181 AC: 2766 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3470

East Asian (EAS) AF: 0.0881 AC: 456 AN: 5178

South Asian (SAS) AF: 0.204 AC: 983 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3025 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13675 AN: 67966

Other (OTH) AF: 0.282 AC: 596 AN: 2114

Alfa AF: 0.251 Hom.: 2440

Bravo AF: 0.302

Asia WGS AF: 0.208 AC: 725 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	1.1
DANN	Benign	0.51
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs7840827; hg19: chr8-41969770;