rs168924

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903693	XR_007065075.1	n.482T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;