rs72977016

Variant names:

• chr3-140651170-C-T
• rs72977016
• ENST00000816745.1:n.224-14819G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000816745.1(CLSTN2-AS1):​n.224-14819G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 151,606 control chromosomes in the GnomAD database, including 50 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 0.021 (50 hom., cov: 30)
• Consequence: CLSTN2-AS1 ENST00000816745.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 4 publications found

Genes affected

CLSTN2-AS1 (HGNC:49095): (CLSTN2 antisense RNA 1)

LOC102724068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.021 (3185/151606) while in subpopulation NFE AF = 0.0303 (2058/67916). AF 95% confidence interval is 0.0292. There are 50 homozygotes in GnomAd4. There are 1512 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 50 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724068	XR_001740934.3	n.509+1776G>A		intron_variant	Intron 3 of 3
LOC102724068	XR_001740935.3	n.487+1798G>A		intron_variant	Intron 3 of 3
LOC102724068	XR_007096116.1	n.265+26569G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLSTN2-AS1	ENST00000816745.1	n.224-14819G>A		intron_variant	Intron 1 of 3
CLSTN2-AS1	ENST00000816746.1	n.237+26569G>A		intron_variant	Intron 1 of 2
CLSTN2-AS1	ENST00000816747.1	n.238-14819G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3189 AN: 151488 Hom.: 50 Cov.: 30

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00291

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0264

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

GnomAD4 genome AF: 0.0210 AC: 3185 AN: 151606 Hom.: 50 Cov.: 30 AF XY: 0.0204 AC XY: 1512 AN XY: 74030

African (AFR) AF: 0.0114 AC: 470 AN: 41342

American (AMR) AF: 0.0192 AC: 292 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3460

East Asian (EAS) AF: 0.000198 AC: 1 AN: 5056

South Asian (SAS) AF: 0.00271 AC: 13 AN: 4804

European-Finnish (FIN) AF: 0.0197 AC: 207 AN: 10486

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0303 AC: 2058 AN: 67916

Other (OTH) AF: 0.0261 AC: 55 AN: 2104

Alfa AF: 0.0284 Hom.: 10

Bravo AF: 0.0202

Asia WGS AF: 0.00289 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.42
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs72977016; hg19: chr3-140370012;