5-67925776-T-G

Position:

• chr5-67925776-T-G

Variant summary

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

The XR_948392.3(LOC105379007):​n.720+95T>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 0.0977 in 152,204 control chromosomes in the GnomAD database, including 933 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 0.098 (933 hom., cov: 32)
• Consequence: LOC105379007 XR_948392.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

LOC105379007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379007	XR_948392.3	n.720+95T>G		intron_variant, non_coding_transcript_variant
LOC105379007	XR_002956213.2	n.525+95T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14876 AN: 152086 Hom.: 934 Cov.: 32

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0609

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0977 AC: 14876 AN: 152204 Hom.: 933 Cov.: 32 AF XY: 0.0966 AC XY: 7186 AN XY: 74422

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.0609

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.122 Hom.: 1713

Bravo AF: 0.0925

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12234107; hg19: chr5-67221604;