5-103617536-C-T

Variant summary

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

The XR_001742831.2(LOC105379107):n.149+10156C>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 0.362 in 151,950 control chromosomes in the GnomAD database, including 10,464 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 0.36 (10464 hom., cov: 32)
• Consequence: LOC105379107 XR_001742831.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379107	XR_001742831.2	n.149+10156C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55039 AN: 151832 Hom.: 10461 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.362 AC: 55076 AN: 151950 Hom.: 10464 Cov.: 32 AF XY: 0.369 AC XY: 27437 AN XY: 74266

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.373

Alfa AF: 0.347 Hom.: 1691

Bravo AF: 0.361

Asia WGS AF: 0.625 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7704545; hg19: chr5-102953237;