10-113970971-A-G

Variant names:

• chr10-113970971-A-G
• rs180934
• ENST00000751600.1:n.127-8729A>G

Variant summary

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

The ENST00000751600.1(ENSG00000297898):​n.127-8729A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,132 control chromosomes in the GnomAD database, including 25,661 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 0.57 (25661 hom., cov: 33)
• Consequence: ENSG00000297898 ENST00000751600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 3 publications found

Genes affected

ENSG00000297898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751600.1. 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
	ENSG00000297898	ENST00000751600.1		n.127-8729A>G		intron	N/A
	ENSG00000297898	ENST00000751601.1		n.58+4333A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86503 AN: 152014 Hom.: 25643 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.569 AC: 86566 AN: 152132 Hom.: 25661 Cov.: 33 AF XY: 0.578 AC XY: 42998 AN XY: 74392

African (AFR) AF: 0.410 AC: 17027 AN: 41480

American (AMR) AF: 0.621 AC: 9489 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2487 AN: 5162

South Asian (SAS) AF: 0.663 AC: 3202 AN: 4826

European-Finnish (FIN) AF: 0.759 AC: 8051 AN: 10606

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42675 AN: 67974

Other (OTH) AF: 0.543 AC: 1150 AN: 2116

Alfa AF: 0.589 Hom.: 4631

Bravo AF: 0.548

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs180934; hg19: chr10-115730730;