rs7137869

Positions:

• chr12-119551841-A-G

Variant summary

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

The ENST00000509470.2(ENSG00000248636):​n.418+1707T>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 0.191 in 151,776 control chromosomes in the GnomAD database, including 3,226 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 0.19 (3226 hom., cov: 32)
• Consequence: ENST00000509470.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370027	XR_007063484.1	n.162+1707T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000509470.2	n.418+1707T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000537366.5	n.235+1707T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000535511.5	n.157+1707T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000665601.1	n.159+1707T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28998 AN: 151656 Hom.: 3218 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.191 AC: 29024 AN: 151776 Hom.: 3226 Cov.: 32 AF XY: 0.190 AC XY: 14072 AN XY: 74142

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.170

Alfa AF: 0.191 Hom.: 3316

Bravo AF: 0.188

Asia WGS AF: 0.154 AC: 533 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7137869; hg19: chr12-119989646;