rs2493624

Variant names:

• chr10-18773327-A-C
• rs2493624
• ENST00000723466.1:n.54-4965A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-18773327-A-C
• chr10-18773327-A-T

Variant summary

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

The ENST00000723466.1(ENSG00000234244):​n.54-4965A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,056 control chromosomes in the GnomAD database, including 6,355 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 0.29 (6355 hom., cov: 32)
• Consequence: ENSG00000234244 ENST00000723466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 3 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723466.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234244	ENST00000723466.1		n.54-4965A>C		intron	N/A
	ENSG00000234244	ENST00000723467.1		n.61-4965A>C		intron	N/A
	ENSG00000234244	ENST00000723468.1		n.205-4965A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43454 AN: 151938 Hom.: 6354 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.286 AC: 43479 AN: 152056 Hom.: 6355 Cov.: 32 AF XY: 0.285 AC XY: 21185 AN XY: 74320

African (AFR) AF: 0.315 AC: 13081 AN: 41464

American (AMR) AF: 0.316 AC: 4828 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2183 AN: 5156

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4816

European-Finnish (FIN) AF: 0.256 AC: 2707 AN: 10588

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17770 AN: 67974

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.266 Hom.: 2881

Bravo AF: 0.299

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.77
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2493624;

hg19: chr10-19062256;