12-75679777-T-C

Position:

• chr12-75679777-T-C

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.401+12328A>G 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 0.0937 in 152,000 control chromosomes in the GnomAD database, including 737 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 0.094 (737 hom., cov: 31)
• Consequence: ENST00000552856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

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 (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369844	XR_007063375.1	n.1371+12328A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063374.1	n.691+12328A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063376.1	n.2298+12328A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063377.1	n.2298+12328A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552856.1	n.401+12328A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000651075.1	n.322+8881T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14240 AN: 151882 Hom.: 736 Cov.: 31

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0937 AC: 14248 AN: 152000 Hom.: 737 Cov.: 31 AF XY: 0.0938 AC XY: 6965 AN XY: 74272

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.0842

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.111

Alfa AF: 0.109 Hom.: 138

Bravo AF: 0.0909

Asia WGS AF: 0.0670 AC: 232 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	3.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12826237; hg19: chr12-76073557;