rs37545

chr5-82938978-G-Achr5-82938978-G-Cchr5-82938978-G-T

Variant summary

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

The XR_001742769.3(LOC105379051):n.374-17865C>T 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 0.561 in 151,940 control chromosomes in the GnomAD database, including 24,688 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 0.56 (24688 hom., cov: 32)
• Consequence: LOC105379051 XR_001742769.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

LOC105379051 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379051	XR_001742769.3	n.374-17865C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85221 AN: 151820 Hom.: 24691 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.561 AC: 85240 AN: 151940 Hom.: 24688 Cov.: 32 AF XY: 0.565 AC XY: 41963 AN XY: 74308

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.525

Alfa AF: 0.594 Hom.: 55278

Bravo AF: 0.538

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.51
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37545; hg19: chr5-82234797;