rs10180496

Variant names:

• chr2-12828774-A-G
• rs10180496
• ENST00000663507.1:n.433-41794T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-12828774-A-G
• chr2-12828774-A-T

Variant summary

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

The ENST00000663507.1(ENSG00000225649):​n.433-41794T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,184 control chromosomes in the GnomAD database, including 2,369 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 (2369 hom., cov: 32)
• Consequence: ENSG00000225649 ENST00000663507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 4 publications found

Genes affected

ENSG00000225649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663507.1. 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
	ENSG00000225649	ENST00000663507.1		n.433-41794T>C		intron	N/A
	ENSG00000225649	ENST00000848763.1		n.320-41794T>C		intron	N/A
	ENSG00000225649	ENST00000848764.1		n.324+87053T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21800 AN: 152066 Hom.: 2364 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.144 AC: 21841 AN: 152184 Hom.: 2369 Cov.: 32 AF XY: 0.137 AC XY: 10156 AN XY: 74398

African (AFR) AF: 0.310 AC: 12847 AN: 41468

American (AMR) AF: 0.0683 AC: 1045 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.0880 AC: 456 AN: 5184

South Asian (SAS) AF: 0.0729 AC: 351 AN: 4816

European-Finnish (FIN) AF: 0.0522 AC: 554 AN: 10604

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0847 AC: 5765 AN: 68024

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.105 Hom.: 3803

Bravo AF: 0.153

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.15

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: rs10180496;

hg19: chr2-12968900;