rs10495523

Variant names:

• chr2-5753937-G-A
• rs10495523
• ENST00000829845.1:n.328+11580G>A

Variant summary

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

The ENST00000829845.1(ENSG00000236106):​n.328+11580G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,212 control chromosomes in the GnomAD database, including 2,110 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 0.14 (2110 hom., cov: 33)
• Consequence: ENSG00000236106 ENST00000829845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 1 publications found

Genes affected

ENSG00000236106 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829845.1. 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
	ENSG00000236106	ENST00000829845.1		n.328+11580G>A		intron	N/A
	ENSG00000236106	ENST00000829846.1		n.317+11580G>A		intron	N/A
	ENSG00000236106	ENST00000829848.1		n.298-4607G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21402 AN: 152094 Hom.: 2102 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.141 AC: 21441 AN: 152212 Hom.: 2110 Cov.: 33 AF XY: 0.144 AC XY: 10726 AN XY: 74430

African (AFR) AF: 0.226 AC: 9368 AN: 41506

American (AMR) AF: 0.169 AC: 2579 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2337 AN: 5162

South Asian (SAS) AF: 0.120 AC: 580 AN: 4818

European-Finnish (FIN) AF: 0.0887 AC: 942 AN: 10618

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5018 AN: 68018

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.109 Hom.: 211

Bravo AF: 0.152

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.29
PhyloP100		-0.88

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: rs10495523;

hg19: chr2-5894069;