rs7726515

Positions:

• chr5-130372657-G-A
• chr5-130372657-G-C

Variant summary

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

The XR_001742880.1(LOC105379171):​n.999+4334G>A 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 0.197 in 151,974 control chromosomes in the GnomAD database, including 3,085 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 0.20 (3085 hom., cov: 31)
• Consequence: LOC105379171 XR_001742880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

LOC105379171 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379171	XR_001742880.1	n.999+4334G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29989 AN: 151856 Hom.: 3085 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.197 AC: 29993 AN: 151974 Hom.: 3085 Cov.: 31 AF XY: 0.198 AC XY: 14699 AN XY: 74278

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.155

Alfa AF: 0.206 Hom.: 6590

Bravo AF: 0.186

Asia WGS AF: 0.183 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7726515; hg19: chr5-129708350;