12-91593828-G-A

Position:

• chr12-91593828-G-A

Variant summary

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

The ENST00000685093.1(ENSG00000289605):​n.503+39897C>T 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 0.112 in 152,024 control chromosomes in the GnomAD database, including 1,239 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 0.11 (1239 hom., cov: 32)
• Consequence: ENST00000685093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369896	XR_001749251.2	n.3670+39897C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685093.1	n.503+39897C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17011 AN: 151904 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.112 AC: 17008 AN: 152024 Hom.: 1239 Cov.: 32 AF XY: 0.109 AC XY: 8131 AN XY: 74300

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.129

Alfa AF: 0.129 Hom.: 257

Bravo AF: 0.105

Asia WGS AF: 0.0370 AC: 129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11106204; hg19: chr12-91987605;