XR_002959376.2:n.4503T>G

Variant names:

• chr2-26303551-T-G
• rs6753473
• XR_002959376.2:n.4503T>G

Variant summary

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

The XR_002959376.2(LOC105374334):​n.4503T>G 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 0.0922 in 152,082 control chromosomes in the GnomAD database, including 1,478 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 0.092 (1478 hom., cov: 32)
• Consequence: LOC105374334 XR_002959376.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 5 publications found

Genes affected

LOC105374334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374334	XR_002959376.2	n.4503T>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105374334	XR_939853.3	n.4503T>G		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105374334	XR_939854.3	n.4503T>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286707	ENST00000653720.1	n.58-280T>G		intron_variant	Intron 1 of 1
ENSG00000286707	ENST00000661577.1	n.216-280T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 13998 AN: 151964 Hom.: 1477 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.00727

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0922 AC: 14019 AN: 152082 Hom.: 1478 Cov.: 32 AF XY: 0.0897 AC XY: 6670 AN XY: 74352

African (AFR) AF: 0.261 AC: 10829 AN: 41426

American (AMR) AF: 0.0483 AC: 737 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3472

East Asian (EAS) AF: 0.0514 AC: 266 AN: 5180

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4816

European-Finnish (FIN) AF: 0.00727 AC: 77 AN: 10594

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0250 AC: 1699 AN: 68002

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.106 Hom.: 784

Bravo AF: 0.105

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.17
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6753473; hg19: chr2-26526419;