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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985017	XR_001752776.2	n.*158C>T		downstream_gene_variant

Ensembl

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

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 v4.3

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;