rs10184321

Variant names:

• chr2-12830246-A-C
• rs10184321
• ENST00000663507.1:n.433-43266T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-12830246-A-C
• chr2-12830246-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.433-43266T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,066 control chromosomes in the GnomAD database, including 27,322 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 0.59 (27322 hom., cov: 32)
• Consequence: ENSG00000225649 ENST00000663507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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.433-43266T>G		intron	N/A
	ENSG00000225649	ENST00000848763.1		n.320-43266T>G		intron	N/A
	ENSG00000225649	ENST00000848764.1		n.324+85581T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90343 AN: 151948 Hom.: 27272 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.595 AC: 90446 AN: 152066 Hom.: 27322 Cov.: 32 AF XY: 0.596 AC XY: 44291 AN XY: 74322

African (AFR) AF: 0.647 AC: 26819 AN: 41476

American (AMR) AF: 0.519 AC: 7942 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2015 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4365 AN: 5148

South Asian (SAS) AF: 0.628 AC: 3028 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6946 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37472 AN: 67972

Other (OTH) AF: 0.575 AC: 1212 AN: 2106

Alfa AF: 0.515 Hom.: 2810

Bravo AF: 0.588

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.28

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: rs10184321;

hg19: chr2-12970372;