rs1160166

Variant names:

• chr16-62915059-C-T
• rs1160166
• ENST00000735360.1:n.264-7698C>T

Variant summary

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

The ENST00000735360.1(ENSG00000296008):​n.264-7698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,874 control chromosomes in the GnomAD database, including 23,702 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 0.54 (23702 hom., cov: 32)
• Consequence: ENSG00000296008 ENST00000735360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 4 publications found

Genes affected

ENSG00000296008 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 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
ENSG00000296008	ENST00000735360.1	n.264-7698C>T		intron_variant	Intron 4 of 6
ENSG00000296008	ENST00000735361.1	n.264-7698C>T		intron_variant	Intron 4 of 5
ENSG00000296008	ENST00000735362.1	n.391-7698C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81297 AN: 151756 Hom.: 23645 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.536 AC: 81419 AN: 151874 Hom.: 23702 Cov.: 32 AF XY: 0.534 AC XY: 39613 AN XY: 74206

African (AFR) AF: 0.756 AC: 31383 AN: 41486

American (AMR) AF: 0.617 AC: 9417 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1328 AN: 5150

South Asian (SAS) AF: 0.399 AC: 1918 AN: 4806

European-Finnish (FIN) AF: 0.401 AC: 4219 AN: 10532

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29437 AN: 67876

Other (OTH) AF: 0.529 AC: 1111 AN: 2100

Alfa AF: 0.471 Hom.: 75012

Bravo AF: 0.564

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.18
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1160166; hg19: chr16-62948963;