12-75848895-A-G

Position:

• chr12-75848895-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552856.1(ENSG00000258077):​n.296-71365T>C 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 0.481 in 152,060 control chromosomes in the GnomAD database, including 18,179 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 0.48 (18179 hom., cov: 32)
• Consequence: ENST00000552856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 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
	ENST00000552856.1	n.296-71365T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73198 AN: 151942 Hom.: 18191 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.481 AC: 73208 AN: 152060 Hom.: 18179 Cov.: 32 AF XY: 0.486 AC XY: 36113 AN XY: 74348

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.498

Alfa AF: 0.499 Hom.: 2428

Bravo AF: 0.467

Asia WGS AF: 0.472 AC: 1642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12230172; hg19: chr12-76242675;