10-97337434-G-A

Variant names:

• chr10-97337434-G-A
• rs4917766
• ENST00000445808.5:n.408+2463G>A

Variant summary

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

The ENST00000445808.5(ENSG00000225850):​n.408+2463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,848 control chromosomes in the GnomAD database, including 21,028 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 0.50 (21028 hom., cov: 30)
• Consequence: ENSG00000225850 ENST00000445808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 11 publications found

Genes affected

ENSG00000225850 (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 = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445808.5. 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
	LOC105378448	NR_188201.1		n.126+2463G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225850	ENST00000445808.5	TSL:3	n.408+2463G>A		intron	N/A
	ENSG00000225850	ENST00000813501.1		n.183-1289G>A		intron	N/A
	ENSG00000225850	ENST00000813502.1		n.127-641G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76342 AN: 151736 Hom.: 21036 Cov.: 30

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.503 AC: 76343 AN: 151848 Hom.: 21028 Cov.: 30 AF XY: 0.508 AC XY: 37676 AN XY: 74188

African (AFR) AF: 0.252 AC: 10439 AN: 41428

American (AMR) AF: 0.590 AC: 9008 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2424 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3527 AN: 5144

South Asian (SAS) AF: 0.587 AC: 2819 AN: 4806

European-Finnish (FIN) AF: 0.576 AC: 6063 AN: 10530

Middle Eastern (MID) AF: 0.648 AC: 184 AN: 284

European-Non Finnish (NFE) AF: 0.590 AC: 40059 AN: 67916

Other (OTH) AF: 0.560 AC: 1178 AN: 2104

Alfa AF: 0.563 Hom.: 90283

Bravo AF: 0.494

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.50
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs4917766; hg19: chr10-99097191;