rs7972859

Positions:

• chr12-119552240-C-T

Variant summary

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

The ENST00000509470.2(ENSG00000248636):​n.418+1308G>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 0.15 in 151,654 control chromosomes in the GnomAD database, including 2,138 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 0.15 (2138 hom., cov: 32)
• Consequence: ENST00000509470.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370027	XR_007063484.1	n.162+1308G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509470.2	n.418+1308G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000537366.5	n.235+1308G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000535511.5	n.157+1308G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000665601.1	n.159+1308G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22783 AN: 151536 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.150 AC: 22791 AN: 151654 Hom.: 2138 Cov.: 32 AF XY: 0.149 AC XY: 11045 AN XY: 74062

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.132

Alfa AF: 0.160 Hom.: 594

Bravo AF: 0.144

Asia WGS AF: 0.134 AC: 466 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7972859; hg19: chr12-119990045;