rs17485426

Variant names:

• chr10-8661044-A-C
• rs17485426
• ENST00000750870.1:n.102-1828T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000750870.1(ENSG00000297769):​n.102-1828T>G variant causes a intron change. The variant allele was found at a frequency of 0.149 in 152,158 control chromosomes in the GnomAD database, including 1,974 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 0.15 (1974 hom., cov: 32)
• Consequence: ENSG00000297769 ENST00000750870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.90
• Publications: 1 publications found

Genes affected

ENSG00000297769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750870.1. 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
	ENSG00000297769	ENST00000750870.1		n.102-1828T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22665 AN: 152040 Hom.: 1977 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.149 AC: 22651 AN: 152158 Hom.: 1974 Cov.: 32 AF XY: 0.146 AC XY: 10832 AN XY: 74400

African (AFR) AF: 0.0785 AC: 3260 AN: 41508

American (AMR) AF: 0.153 AC: 2332 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3468

East Asian (EAS) AF: 0.0747 AC: 386 AN: 5168

South Asian (SAS) AF: 0.103 AC: 496 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10592

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13727 AN: 68000

Other (OTH) AF: 0.170 AC: 359 AN: 2116

Alfa AF: 0.186 Hom.: 1418

Bravo AF: 0.153

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	22
DANN	Benign	0.73
PhyloP100		3.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17485426;

hg19: chr10-8703007;