rs10845697

Variant names:

• chr12-13031952-G-A
• rs10845697
• ENST00000543321.1:n.1174-7498G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-13031952-G-A
• chr12-13031952-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000543321.1(ENSG00000255621):​n.1174-7498G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,820 control chromosomes in the GnomAD database, including 17,487 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 0.46 (17487 hom., cov: 31)
• Consequence: ENSG00000255621 ENST00000543321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

ENSG00000255621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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
ENSG00000255621	ENST00000543321.1	n.1174-7498G>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69638 AN: 151702 Hom.: 17454 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.459 AC: 69731 AN: 151820 Hom.: 17487 Cov.: 31 AF XY: 0.459 AC XY: 34030 AN XY: 74212

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.472

Alfa AF: 0.416 Hom.: 2383

Bravo AF: 0.482

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10845697; hg19: chr12-13184886;