5-132053814-T-C

Position:

• chr5-132053814-T-C

Variant summary

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

The XR_001742531.2(LOC105379174):​n.212-210A>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 0.567 in 151,938 control chromosomes in the GnomAD database, including 24,614 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 0.57 (24614 hom., cov: 32)
• Consequence: LOC105379174 XR_001742531.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

LOC105379174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379174	XR_001742531.2	n.212-210A>G		intron_variant, non_coding_transcript_variant
LOC105379174	XR_948785.3	n.229-210A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86049 AN: 151820 Hom.: 24588 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.567 AC: 86124 AN: 151938 Hom.: 24614 Cov.: 32 AF XY: 0.559 AC XY: 41533 AN XY: 74234

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.566

Alfa AF: 0.486 Hom.: 1880

Bravo AF: 0.570

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31400; hg19: chr5-131389507;