chr12-115586256-T-C

Position:

• chr12-115586256-T-C

Variant summary

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

The ENST00000551940.1(ENSG00000257407):​n.344-3291A>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 0.786 in 152,132 control chromosomes in the GnomAD database, including 47,250 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 0.79 (47250 hom., cov: 31)
• Consequence: ENST00000551940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

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 (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370003	XR_945389.3	n.119-77842A>G		intron_variant, non_coding_transcript_variant
LOC105370003	XR_945388.3	n.119-77842A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000551940.1	n.344-3291A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000551531.1	n.177-3291A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119567 AN: 152012 Hom.: 47222 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.786 AC: 119641 AN: 152132 Hom.: 47250 Cov.: 31 AF XY: 0.790 AC XY: 58726 AN XY: 74358

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.787

Alfa AF: 0.803 Hom.: 55799

Bravo AF: 0.780

Asia WGS AF: 0.862 AC: 2995 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	2.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10735088; hg19: chr12-116024061;