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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376400	XR_001747277.2	n.99-1828T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297769	ENST00000750870.1	n.102-1828T>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs17485426; hg19: chr10-8703007;