chr1-82435581-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000650063.1		n.887+119568T>G		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.719+119568T>G		intron	N/A

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

African (AFR) AF: 0.375 AC: 15551 AN: 41444

American (AMR) AF: 0.0847 AC: 1295 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3466

East Asian (EAS) AF: 0.107 AC: 554 AN: 5182

South Asian (SAS) AF: 0.101 AC: 488 AN: 4826

European-Finnish (FIN) AF: 0.0629 AC: 667 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4088 AN: 68022

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.0824 Hom.: 1786

Bravo AF: 0.164

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.10

Splicing

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

Other links and lift over

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