8-121112062-A-G

Variant names:

• chr8-121112062-A-G
• rs2196051
• ENST00000517739.1:n.259-7175A>G

Variant summary

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

The ENST00000517739.1(ENSG00000253619):​n.259-7175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,048 control chromosomes in the GnomAD database, including 27,600 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 0.54 (27600 hom., cov: 32)
• Consequence: ENSG00000253619 ENST00000517739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 10 publications found

Genes affected

ENSG00000253619 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517739.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253619	ENST00000517739.1	TSL:5	n.259-7175A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82326 AN: 151930 Hom.: 27518 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.542 AC: 82474 AN: 152048 Hom.: 27600 Cov.: 32 AF XY: 0.551 AC XY: 40977 AN XY: 74320

African (AFR) AF: 0.883 AC: 36631 AN: 41488

American (AMR) AF: 0.575 AC: 8792 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5163 AN: 5180

South Asian (SAS) AF: 0.775 AC: 3728 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3666 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21804 AN: 67950

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.412 Hom.: 36681

Bravo AF: 0.570

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.93
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2196051; hg19: chr8-122124302;