rs1567147

Variant names:

• chr16-7997956-A-G
• rs1567147
• ENST00000567103.2:n.381+9189T>C

Variant summary

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

The ENST00000567103.2(ENSG00000260289):​n.381+9189T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,354 control chromosomes in the GnomAD database, including 111 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 0.032 (111 hom., cov: 33)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

Genes affected

ENSG00000260289 (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 (EAS) allele frequency at 95% confidence interval = 0.114 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
ENSG00000260289	ENST00000567103.2	n.381+9189T>C		intron_variant	Intron 2 of 3	5
ENSG00000260289	ENST00000654046.1	n.414+9189T>C		intron_variant	Intron 2 of 3
ENSG00000260289	ENST00000670665.1	n.414+9189T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4902 AN: 152236 Hom.: 110 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0180

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0323 AC: 4918 AN: 152354 Hom.: 111 Cov.: 33 AF XY: 0.0335 AC XY: 2496 AN XY: 74506

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.0283

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0180

Gnomad4 NFE AF: 0.0254

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0289 Hom.: 29

Bravo AF: 0.0330

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.041
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567147; hg19: chr16-8047958;