rs12103880

Positions:

• chr17-9795025-G-A

Variant summary

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

The ENST00000634974.2(ENSG00000282882):​n.283-8758G>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 0.251 in 152,114 control chromosomes in the GnomAD database, including 5,774 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 0.25 (5774 hom., cov: 32)
• Consequence: ENST00000634974.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634974.2	n.283-8758G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38093 AN: 151998 Hom.: 5771 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.251 AC: 38140 AN: 152114 Hom.: 5774 Cov.: 32 AF XY: 0.241 AC XY: 17930 AN XY: 74338

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.0913

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.221

Alfa AF: 0.210 Hom.: 7335

Bravo AF: 0.257

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12103880; hg19: chr17-9698342; COSMIC: COSV57652492;