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. Variant got -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

Genes affected

ENSG00000225649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225649	ENST00000663507.1	n.433-43266T>G		intron_variant	Intron 4 of 6

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

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.575

Alfa AF: 0.510 Hom.: 2651

Bravo AF: 0.588

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10184321; hg19: chr2-12970372;