12-75655245-C-T

Position:

• chr12-75655245-C-T

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.402-23931G>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 0.535 in 151,958 control chromosomes in the GnomAD database, including 22,237 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 0.54 (22237 hom., cov: 31)
• Consequence: ENST00000552856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369844	XR_007063375.1	n.1590+3799G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063374.1	n.692-23931G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063376.1	n.2517+3799G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063377.1	n.2517+3799G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552856.1	n.402-23931G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000651075.1	n.201+2819C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81260 AN: 151840 Hom.: 22214 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.535 AC: 81332 AN: 151958 Hom.: 22237 Cov.: 31 AF XY: 0.535 AC XY: 39745 AN XY: 74278

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.507

Alfa AF: 0.563 Hom.: 12612

Bravo AF: 0.521

Asia WGS AF: 0.453 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10735989; hg19: chr12-76049025;