rs2347699

Variant names:

• chr7-134706212-T-A
• rs2347699
• XR_007060535.1:n.29222-39122A>T

Variant summary

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

The XR_007060535.1(LOC124901750):​n.29222-39122A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,052 control chromosomes in the GnomAD database, including 6,554 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 0.29 (6554 hom., cov: 32)
• Consequence: LOC124901750 XR_007060535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 1 publications found

Genes affected

LOC124901750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 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: 0.291 AC: 44174 AN: 151934 Hom.: 6538 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.291 AC: 44226 AN: 152052 Hom.: 6554 Cov.: 32 AF XY: 0.288 AC XY: 21378 AN XY: 74336

African (AFR) AF: 0.333 AC: 13793 AN: 41480

American (AMR) AF: 0.341 AC: 5213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3470

East Asian (EAS) AF: 0.193 AC: 995 AN: 5164

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2117 AN: 10582

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18942 AN: 67952

Other (OTH) AF: 0.281 AC: 592 AN: 2110

Alfa AF: 0.288 Hom.: 810

Bravo AF: 0.303

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.85
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2347699; hg19: chr7-134390964;