rs10437024

Variant names:

• chr1-82435581-A-C
• rs10437024
• ENST00000650063.1:n.887+119568T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650063.1(ENSG00000233290):​n.887+119568T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,142 control chromosomes in the GnomAD database, including 3,228 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 (3228 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233290	ENST00000650063.1	n.887+119568T>G		intron_variant	Intron 6 of 6
ENSG00000233290	ENST00000653483.1	n.719+119568T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23237 AN: 152024 Hom.: 3205 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.153 AC: 23304 AN: 152142 Hom.: 3228 Cov.: 32 AF XY: 0.152 AC XY: 11300 AN XY: 74390

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0776 Hom.: 1208

Bravo AF: 0.164

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10437024; hg19: chr1-82901264; COSMIC: COSV59964125;