2-18651080-C-A

Variant names:

• chr2-18651080-C-A
• rs12053481
• XR_007086230.1:n.8361C>A

Variant summary

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

The XR_007086230.1(LOC105373456):​n.8361C>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 0.137 in 152,028 control chromosomes in the GnomAD database, including 2,084 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 0.14 (2084 hom., cov: 32)
• Consequence: LOC105373456 XR_007086230.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 2 publications found

Genes affected

LOC105373456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373456	XR_007086230.1	n.8361C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373456	XR_001739304.3	n.853+6780C>A		intron_variant	Intron 3 of 5
LOC105373456	XR_001739311.2	n.368+6780C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304698	ENST00000805686.1	n.610+6780C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20801 AN: 151910 Hom.: 2078 Cov.: 32

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.137 AC: 20823 AN: 152028 Hom.: 2084 Cov.: 32 AF XY: 0.139 AC XY: 10351 AN XY: 74302

African (AFR) AF: 0.0410 AC: 1700 AN: 41482

American (AMR) AF: 0.244 AC: 3718 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2319 AN: 5148

South Asian (SAS) AF: 0.0879 AC: 423 AN: 4812

European-Finnish (FIN) AF: 0.119 AC: 1251 AN: 10544

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10238 AN: 67992

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.150 Hom.: 6125

Bravo AF: 0.149

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.40
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs12053481; hg19: chr2-18832346;