rs12918773

Positions:

• chr16-89674995-G-A

Variant summary

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

The ENST00000615131.2(ENSG00000275734):​n.1300+2128G>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 0.0762 in 151,656 control chromosomes in the GnomAD database, including 530 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 0.076 (530 hom., cov: 29)
• Consequence: ENST00000615131.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615131.2	n.1300+2128G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11552 AN: 151536 Hom.: 529 Cov.: 29

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0762 AC: 11557 AN: 151656 Hom.: 530 Cov.: 29 AF XY: 0.0784 AC XY: 5807 AN XY: 74086

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0767 Hom.: 404

Bravo AF: 0.0757

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12918773; hg19: chr16-89741403;