chr16-55655632-A-G

Variant names:

• chr16-55655632-A-G
• rs168924
• XR_007065075.1:n.482T>C

Variant summary

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

The XR_007065075.1(LOC124903693):​n.482T>C 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 0.157 in 152,320 control chromosomes in the GnomAD database, including 2,017 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 0.16 (2016 hom., cov: 33)
  • Exomes 𝑓: 0.085 (1 hom.)
• Consequence: LOC124903693 XR_007065075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 18 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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: 0.157 AC: 23852 AN: 152108 Hom.: 2015 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.0851 AC: 8 AN: 94 Hom.: 1 Cov.: 0 AF XY: 0.0811 AC XY: 6 AN XY: 74

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.100 AC: 1 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0946 AC: 7 AN: 74

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.157 AC: 23876 AN: 152226 Hom.: 2016 Cov.: 33 AF XY: 0.155 AC XY: 11507 AN XY: 74440

African (AFR) AF: 0.216 AC: 8980 AN: 41526

American (AMR) AF: 0.128 AC: 1958 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3470

East Asian (EAS) AF: 0.142 AC: 733 AN: 5168

South Asian (SAS) AF: 0.0990 AC: 477 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1382 AN: 10606

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9417 AN: 68018

Other (OTH) AF: 0.149 AC: 316 AN: 2116

Alfa AF: 0.149 Hom.: 2241

Bravo AF: 0.161

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		-0.25
PromoterAI		0.024	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs168924; hg19: chr16-55689544;