7-140973634-G-C

Variant names:

• chr7-140973634-G-C
• rs3852286
• XR_002956518.2:n.1628-14395G>C

Variant summary

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

The XR_002956518.2(LOC105375536):​n.1628-14395G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,902 control chromosomes in the GnomAD database, including 37,487 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 0.68 (37487 hom., cov: 30)
• Consequence: LOC105375536 XR_002956518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 6 publications found

Genes affected

LOC105375536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.683 AC: 103743 AN: 151784 Hom.: 37483 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.683 AC: 103774 AN: 151902 Hom.: 37487 Cov.: 30 AF XY: 0.690 AC XY: 51209 AN XY: 74212

African (AFR) AF: 0.419 AC: 17356 AN: 41376

American (AMR) AF: 0.759 AC: 11576 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4653 AN: 5166

South Asian (SAS) AF: 0.800 AC: 3840 AN: 4800

European-Finnish (FIN) AF: 0.826 AC: 8715 AN: 10554

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52585 AN: 67970

Other (OTH) AF: 0.713 AC: 1501 AN: 2104

Alfa AF: 0.711 Hom.: 4957

Bravo AF: 0.664

Asia WGS AF: 0.840 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3852286; hg19: chr7-140673434;