rs11976165

Variant names:

• chr7-56632861-C-T
• rs11976165
• ENST00000796931.1:n.279+17117G>A

Variant summary

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

The ENST00000796931.1(ENSG00000287019):​n.279+17117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,082 control chromosomes in the GnomAD database, including 3,784 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 0.22 (3784 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000287019 ENST00000796931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 publications found

Genes affected

ENSG00000287019 (HGNC:):

TRIM60P16 (HGNC:38488): (tripartite motif containing 60 pseudogene 16)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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
ENSG00000287019	ENST00000796931.1	n.279+17117G>A		intron_variant	Intron 3 of 4
ENSG00000287019	ENST00000796932.1	n.351+17117G>A		intron_variant	Intron 4 of 5
ENSG00000287019	ENST00000796933.1	n.443+17117G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33128 AN: 151964 Hom.: 3772 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0908

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.218 AC: 33164 AN: 152082 Hom.: 3784 Cov.: 33 AF XY: 0.217 AC XY: 16165 AN XY: 74346

African (AFR) AF: 0.276 AC: 11471 AN: 41488

American (AMR) AF: 0.245 AC: 3747 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3464

East Asian (EAS) AF: 0.0907 AC: 470 AN: 5184

South Asian (SAS) AF: 0.204 AC: 985 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1788 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13362 AN: 67984

Other (OTH) AF: 0.200 AC: 421 AN: 2108

Alfa AF: 0.215 Hom.: 625

Bravo AF: 0.227

Asia WGS AF: 0.174 AC: 604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.33
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs11976165; hg19: chr7-56700554; COSMIC: COSV101466844;