chr5-7906794-G-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;