rs10492744

Variant names:

• chr13-44879490-T-C
• rs10492744
• ENST00000807128.1:n.442+8530A>G

Variant summary

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

The ENST00000807128.1(ENSG00000304924):​n.442+8530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,078 control chromosomes in the GnomAD database, including 3,227 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 0.12 (3227 hom., cov: 32)
• Consequence: ENSG00000304924 ENST00000807128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 0 publications found

Genes affected

ENSG00000304924 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370187	XR_941934.4	n.653+8530A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304924	ENST00000807128.1	n.442+8530A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18523 AN: 151960 Hom.: 3210 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00246

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.122 AC: 18593 AN: 152078 Hom.: 3227 Cov.: 32 AF XY: 0.121 AC XY: 8966 AN XY: 74378

African (AFR) AF: 0.388 AC: 16057 AN: 41436

American (AMR) AF: 0.0891 AC: 1361 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3470

East Asian (EAS) AF: 0.0946 AC: 490 AN: 5182

South Asian (SAS) AF: 0.0585 AC: 281 AN: 4806

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10600

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00246 AC: 167 AN: 67988

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0730 Hom.: 242

Bravo AF: 0.141

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.47
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10492744; hg19: chr13-45453625;