rs7212734

Variant names:

• chr17-6437140-G-A
• rs7212734
• XR_001752776.2:n.*158C>T

Variant summary

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

The XR_001752776.2(LOC107985017):​n.*158C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,996 control chromosomes in the GnomAD database, including 9,290 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 0.32 (9290 hom., cov: 31)
• Consequence: LOC107985017 XR_001752776.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 4 publications found

Genes affected

LOC107985017 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.324 AC: 49203 AN: 151878 Hom.: 9299 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.324 AC: 49189 AN: 151996 Hom.: 9290 Cov.: 31 AF XY: 0.320 AC XY: 23787 AN XY: 74274

African (AFR) AF: 0.132 AC: 5467 AN: 41462

American (AMR) AF: 0.380 AC: 5794 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1081 AN: 5148

South Asian (SAS) AF: 0.324 AC: 1561 AN: 4814

European-Finnish (FIN) AF: 0.319 AC: 3364 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29218 AN: 67964

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.332 Hom.: 1784

Bravo AF: 0.317

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.3
DANN	Benign	0.40
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs7212734; hg19: chr17-6340460;