16-55653300-G-T

Position:

• chr16-55653300-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903693	XR_007065075.1	n.1155C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.486

Alfa AF: 0.482 Hom.: 16397

Bravo AF: 0.476

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4783899; hg19: chr16-55687212;