16-85977427-C-T

Variant names:

• chr16-85977427-C-T
• rs13333054
• XR_007065161.1:n.7682G>A

Variant summary

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

The XR_007065161.1(LOC124903741):​n.7682G>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 0.237 in 152,080 control chromosomes in the GnomAD database, including 4,741 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 0.24 (4741 hom., cov: 33)
• Consequence: LOC124903741 XR_007065161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 41 publications found

Genes affected

LOC124903741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645754.1. 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
	ENSG00000285040	ENST00000645754.1		n.227+7015G>A		intron	N/A
	ENSG00000294410	ENST00000723428.1		n.410-108C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36048 AN: 151962 Hom.: 4727 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.237 AC: 36093 AN: 152080 Hom.: 4741 Cov.: 33 AF XY: 0.238 AC XY: 17685 AN XY: 74334

African (AFR) AF: 0.218 AC: 9050 AN: 41488

American (AMR) AF: 0.379 AC: 5791 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2333 AN: 5168

South Asian (SAS) AF: 0.193 AC: 928 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1791 AN: 10582

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14741 AN: 67970

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.225 Hom.: 12037

Bravo AF: 0.261

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs13333054; hg19: chr16-86011033;