rs13225058

chr7-140246253-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745386.2(LOC107986854):n.137-7303A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,954 control chromosomes in the GnomAD database, including 7,561 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 0.30 (7561 hom., cov: 31)
• Consequence: LOC107986854 XR_001745386.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

Genes affected

LOC107986854 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986854	XR_001745386.2	n.137-7303A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46108 AN: 151836 Hom.: 7559 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.303 AC: 46114 AN: 151954 Hom.: 7561 Cov.: 31 AF XY: 0.299 AC XY: 22190 AN XY: 74246

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.293

Alfa AF: 0.342 Hom.: 4286

Bravo AF: 0.319

Asia WGS AF: 0.304 AC: 1055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	9.6
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13225058; hg19: chr7-139946053; COSMIC: COSV63019555;