rs10493293

Variant names:

• chr1-60673496-G-A
• rs10493293
• ENST00000423403.1:n.464-10471C>T

Variant summary

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

The ENST00000423403.1(ENSG00000231252):​n.464-10471C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,144 control chromosomes in the GnomAD database, including 542 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 0.059 (542 hom., cov: 33)
• Consequence: ENSG00000231252 ENST00000423403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 1 publications found

Genes affected

ENSG00000231252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101926964	NR_110628.1	n.464-10471C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231252	ENST00000423403.1	n.464-10471C>T		intron_variant	Intron 4 of 5	2
ENSG00000231252	ENST00000634701.1	n.954+3700C>T		intron_variant	Intron 9 of 9	5
ENSG00000231252	ENST00000635290.1	n.727+3700C>T		intron_variant	Intron 7 of 8	5

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8942 AN: 152026 Hom.: 538 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00957

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0590 AC: 8976 AN: 152144 Hom.: 542 Cov.: 33 AF XY: 0.0594 AC XY: 4422 AN XY: 74392

African (AFR) AF: 0.155 AC: 6437 AN: 41478

American (AMR) AF: 0.0438 AC: 670 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.0718 AC: 370 AN: 5150

South Asian (SAS) AF: 0.0586 AC: 282 AN: 4814

European-Finnish (FIN) AF: 0.0385 AC: 408 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00957 AC: 651 AN: 68020

Other (OTH) AF: 0.0440 AC: 93 AN: 2116

Alfa AF: 0.0313 Hom.: 643

Bravo AF: 0.0633

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.75
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10493293; hg19: chr1-61139168;