5-41126148-G-C

Position:

• chr5-41126148-G-C

Variant summary

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

The XR_001742650.2(LOC105374739):​n.886+12325G>C 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 0.252 in 152,142 control chromosomes in the GnomAD database, including 5,816 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 0.25 (5816 hom., cov: 33)
• Consequence: LOC105374739 XR_001742650.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

LOC105374739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374739	XR_001742650.2	n.886+12325G>C		intron_variant, non_coding_transcript_variant
LOC105374739	XR_001742651.2	n.296+12325G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38316 AN: 152024 Hom.: 5817 Cov.: 33

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.252 AC: 38308 AN: 152142 Hom.: 5816 Cov.: 33 AF XY: 0.252 AC XY: 18760 AN XY: 74356

Gnomad4 AFR AF: 0.0905

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.272

Alfa AF: 0.208 Hom.: 574

Bravo AF: 0.228

Asia WGS AF: 0.140 AC: 487 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512762; hg19: chr5-41126250;