rs55768522

Variant names:

• chr9-114811940-G-A
• rs55768522
• ENST00000776746.1:n.516C>T

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.516C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,168 control chromosomes in the GnomAD database, including 544 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 0.046 (544 hom., cov: 32)
• Consequence: ENSG00000301160 ENST00000776746.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 5 publications found

Genes affected

ENSG00000301160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776746.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301160	ENST00000776746.1		n.516C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7003 AN: 152050 Hom.: 534 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00600

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0463 AC: 7040 AN: 152168 Hom.: 544 Cov.: 32 AF XY: 0.0540 AC XY: 4013 AN XY: 74382

African (AFR) AF: 0.0449 AC: 1864 AN: 41534

American (AMR) AF: 0.128 AC: 1952 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5156

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4812

European-Finnish (FIN) AF: 0.0959 AC: 1014 AN: 10574

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00600 AC: 408 AN: 68000

Other (OTH) AF: 0.0458 AC: 97 AN: 2116

Alfa AF: 0.0382 Hom.: 124

Bravo AF: 0.0532

Asia WGS AF: 0.143 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.50
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55768522;

hg19: chr9-117574220;