chr12-131522286-T-G

Position:

• chr12-131522286-T-G

Variant summary

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

The ENST00000653719.1(ENSG00000256209):​n.204+7405A>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 0.715 in 121,504 control chromosomes in the GnomAD database, including 31,578 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 0.71 (31578 hom., cov: 29)
• Consequence: ENST00000653719.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929974	XR_007063532.1	n.1067+7489A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653719.1	n.204+7405A>C		intron_variant, non_coding_transcript_variant
	ENST00000658806.1	n.114+7489A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.715 AC: 86803 AN: 121454 Hom.: 31566 Cov.: 29

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.715 AC: 86837 AN: 121504 Hom.: 31578 Cov.: 29 AF XY: 0.716 AC XY: 43103 AN XY: 60202

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.670

Alfa AF: 0.401 Hom.: 252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10773917; hg19: chr12-132006831;