5-93151837-T-C

Position:

• chr5-93151837-T-C

Variant summary

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

The XR_007058869.1(LOC105379083):​n.120-1931A>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 0.68 in 152,122 control chromosomes in the GnomAD database, including 35,971 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 (35971 hom., cov: 32)
• Consequence: LOC105379083 XR_007058869.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

LOC105379083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379083	XR_007058869.1	n.120-1931A>G		intron_variant, non_coding_transcript_variant
LOC105379083	XR_948569.3	n.128-1931A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103363 AN: 152004 Hom.: 35922 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.680 AC: 103471 AN: 152122 Hom.: 35971 Cov.: 32 AF XY: 0.688 AC XY: 51197 AN XY: 74372

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.644

Alfa AF: 0.608 Hom.: 25847

Bravo AF: 0.690

Asia WGS AF: 0.751 AC: 2609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13173682; hg19: chr5-92487543;