XR_007086222.1:n.5765C>T

Variant names:

• chr2-12710994-G-A
• rs7607490
• XR_007086222.1:n.5765C>T

Variant summary

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

The XR_007086222.1(LOC124905974):​n.5765C>T 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 0.125 in 152,120 control chromosomes in the GnomAD database, including 1,431 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 0.13 (1431 hom., cov: 32)
• Consequence: LOC124905974 XR_007086222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 8 publications found

Genes affected

LOC124905974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905974	XR_007086222.1	n.5765C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124905974	XR_007086221.1	n.544+5221C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286427	ENST00000657078.2	n.389+5370C>T		intron_variant	Intron 1 of 1
ENSG00000286427	ENST00000840615.1	n.282+5370C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19006 AN: 152002 Hom.: 1433 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.125 AC: 19015 AN: 152120 Hom.: 1431 Cov.: 32 AF XY: 0.120 AC XY: 8922 AN XY: 74372

African (AFR) AF: 0.204 AC: 8446 AN: 41454

American (AMR) AF: 0.0884 AC: 1351 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.127 AC: 608 AN: 4806

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10604

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7314 AN: 67996

Other (OTH) AF: 0.118 AC: 250 AN: 2116

Alfa AF: 0.109 Hom.: 704

Bravo AF: 0.131

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.27
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs7607490; hg19: chr2-12851120;