rs10918425

Variant names:

• chr1-166321824-T-C
• rs10918425
• ENST00000653824.3:n.221-13504T>C

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.221-13504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,234 control chromosomes in the GnomAD database, including 1,483 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 0.080 (1483 hom., cov: 32)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 1 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.179-13504T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229588	ENST00000653824.3	n.221-13504T>C		intron_variant	Intron 1 of 2
ENSG00000229588	ENST00000829274.1	n.179-17076T>C		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829275.1	n.190-13504T>C		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829276.1	n.141-13504T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12205 AN: 152116 Hom.: 1475 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0804 AC: 12243 AN: 152234 Hom.: 1483 Cov.: 32 AF XY: 0.0792 AC XY: 5894 AN XY: 74464

African (AFR) AF: 0.261 AC: 10816 AN: 41482

American (AMR) AF: 0.0507 AC: 775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.0766 AC: 397 AN: 5182

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4826

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10628

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00121 AC: 82 AN: 68024

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0288 Hom.: 192

Bravo AF: 0.0932

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.86
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10918425; hg19: chr1-166291061;