rs10845697

Positions:

• 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, non coding transcript 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: ENST00000543321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000543321.1	n.1174-7498G>A		intron_variant, non_coding_transcript_variant		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;