chr16-55653300-G-T

Variant names:

• chr16-55653300-G-T
• rs4783899
• XR_007065075.1:n.1155C>A

Variant summary

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

The XR_007065075.1(LOC124903693):​n.1155C>A 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 0.474 in 151,988 control chromosomes in the GnomAD database, including 17,296 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 0.47 (17296 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 2 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71963 AN: 151870 Hom.: 17286 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.474 AC: 72009 AN: 151988 Hom.: 17296 Cov.: 32 AF XY: 0.478 AC XY: 35507 AN XY: 74290

African (AFR) AF: 0.416 AC: 17236 AN: 41430

American (AMR) AF: 0.517 AC: 7892 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3462

East Asian (EAS) AF: 0.419 AC: 2166 AN: 5172

South Asian (SAS) AF: 0.589 AC: 2837 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4935 AN: 10548

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33583 AN: 67960

Other (OTH) AF: 0.486 AC: 1027 AN: 2112

Alfa AF: 0.484 Hom.: 21790

Bravo AF: 0.476

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.66
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4783899; hg19: chr16-55687212;