chr16-89674995-G-A

Variant names:

• chr16-89674995-G-A
• rs12918773
• ENST00000615131.2:n.1300+2128G>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 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: ENSG00000275734 ENST00000615131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

ENSG00000275734 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275734	ENST00000615131.2	n.1300+2128G>A		intron_variant	Intron 1 of 2	6

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;