rs7715062

Variant names:

• chr5-7906794-G-T
• rs7715062
• XR_007058683.1:n.2152G>T

Variant summary

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

The XR_007058683.1(LOC124900936):​n.2152G>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 0.355 in 151,676 control chromosomes in the GnomAD database, including 9,963 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 0.35 (9963 hom., cov: 32)
• Consequence: LOC124900936 XR_007058683.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 9 publications found

Genes affected

LOC124900936 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900936	XR_007058683.1	n.2152G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53736 AN: 151558 Hom.: 9950 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.355 AC: 53785 AN: 151676 Hom.: 9963 Cov.: 32 AF XY: 0.352 AC XY: 26070 AN XY: 74100

African (AFR) AF: 0.293 AC: 12146 AN: 41404

American (AMR) AF: 0.282 AC: 4298 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3464

East Asian (EAS) AF: 0.156 AC: 807 AN: 5176

South Asian (SAS) AF: 0.458 AC: 2205 AN: 4810

European-Finnish (FIN) AF: 0.355 AC: 3735 AN: 10520

Middle Eastern (MID) AF: 0.493 AC: 143 AN: 290

European-Non Finnish (NFE) AF: 0.409 AC: 27727 AN: 67774

Other (OTH) AF: 0.365 AC: 766 AN: 2100

Alfa AF: 0.398 Hom.: 6695

Bravo AF: 0.344

Asia WGS AF: 0.335 AC: 1152 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7715062; hg19: chr5-7906907;