XR_949287.4:n.2065T>A

Variant names:

• chr1-234677730-A-T
• rs2987460
• XR_949287.4:n.2065T>A

Variant summary

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

The XR_949287.4(LOC105373208):​n.2065T>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 0.216 in 152,102 control chromosomes in the GnomAD database, including 4,667 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 0.22 (4667 hom., cov: 32)
• Consequence: LOC105373208 XR_949287.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 3 publications found

Genes affected

LOC105373208 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373208	XR_949287.4	n.2065T>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373209	NR_188651.1	n.122+1167A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230628	ENST00000442382.1	n.97-4740T>A		intron_variant	Intron 1 of 1	2
ENSG00000228044	ENST00000449012.2	n.313-3081A>T		intron_variant	Intron 2 of 2	3
ENSG00000228044	ENST00000453568.1	n.32-3081A>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32781 AN: 151984 Hom.: 4647 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.216 AC: 32838 AN: 152102 Hom.: 4667 Cov.: 32 AF XY: 0.214 AC XY: 15874 AN XY: 74344

African (AFR) AF: 0.408 AC: 16903 AN: 41460

American (AMR) AF: 0.183 AC: 2803 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3470

East Asian (EAS) AF: 0.0787 AC: 408 AN: 5182

South Asian (SAS) AF: 0.108 AC: 523 AN: 4830

European-Finnish (FIN) AF: 0.120 AC: 1270 AN: 10590

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9658 AN: 67970

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.170 Hom.: 340

Bravo AF: 0.231

Asia WGS AF: 0.119 AC: 415 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	3.0
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2987460; hg19: chr1-234813476;