rs1567147

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_197430.1(LOC105371069):​n.414+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: LOC105371069 NR_197430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 1 publications found

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_197430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371069	NR_197430.1		n.414+9189T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260289	ENST00000567103.2	TSL:5	n.381+9189T>C		intron	N/A
	ENSG00000260289	ENST00000654046.1		n.414+9189T>C		intron	N/A
	ENSG00000260289	ENST00000670665.1		n.414+9189T>C		intron	N/A

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

African (AFR) AF: 0.0336 AC: 1399 AN: 41576

American (AMR) AF: 0.0283 AC: 433 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3468

East Asian (EAS) AF: 0.122 AC: 632 AN: 5184

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4828

European-Finnish (FIN) AF: 0.0180 AC: 191 AN: 10628

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1726 AN: 68040

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0319 Hom.: 216

Bravo AF: 0.0330

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.041
DANN	Benign	0.69
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1567147; hg19: chr16-8047958;