rs12515335

Positions:

• chr5-8556975-T-C

Variant summary

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

The ENST00000657075.1(ENSG00000249782):​n.689-3102T>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 0.187 in 152,058 control chromosomes in the GnomAD database, including 3,063 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 (3063 hom., cov: 32)
• Consequence: ENST00000657075.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374647	XR_925766.3	n.651-3102T>C		intron_variant, non_coding_transcript_variant
LOC105374647	XR_925767.3	n.641-3102T>C		intron_variant, non_coding_transcript_variant
LOC105374647	XR_925768.3	n.473-3102T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657075.1	n.689-3102T>C		intron_variant, non_coding_transcript_variant
	ENST00000654467.1	n.472-3102T>C		intron_variant, non_coding_transcript_variant
	ENST00000659580.1	n.651-3102T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28456 AN: 151940 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.187 AC: 28479 AN: 152058 Hom.: 3063 Cov.: 32 AF XY: 0.184 AC XY: 13645 AN XY: 74332

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0971

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.218

Alfa AF: 0.219 Hom.: 2770

Bravo AF: 0.181

Asia WGS AF: 0.0680 AC: 236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12515335; hg19: chr5-8557087;