5-103674067-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.150-4445C>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 0.0748 in 152,202 control chromosomes in the GnomAD database, including 710 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 0.075 (710 hom., cov: 33)
• Consequence: LOC105379107 XR_001742831.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379107	XR_001742831.2	n.150-4445C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11395 AN: 152084 Hom.: 715 Cov.: 33

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0748 AC: 11385 AN: 152202 Hom.: 710 Cov.: 33 AF XY: 0.0791 AC XY: 5885 AN XY: 74402

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0761 Hom.: 527

Bravo AF: 0.0729

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.037
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11950651; hg19: chr5-103009768;