rs10876844

Positions:

• chr12-55656922-C-A

Variant summary

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

The ENST00000556606.1(ENSG00000258921):​n.83+2791G>T 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 0.431 in 151,876 control chromosomes in the GnomAD database, including 14,514 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 0.43 (14514 hom., cov: 31)
• Consequence: ENST00000556606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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
	ENST00000556606.1	n.83+2791G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65356 AN: 151758 Hom.: 14491 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.431 AC: 65419 AN: 151876 Hom.: 14514 Cov.: 31 AF XY: 0.438 AC XY: 32472 AN XY: 74192

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.412

Alfa AF: 0.389 Hom.: 11778

Bravo AF: 0.423

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10876844; hg19: chr12-56050706;