rs13134014

chr4-98183728-G-Achr4-98183728-G-T

Variant summary

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

The XR_001741771.2(LOC105377340):n.633+1403C>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 0.16 in 151,990 control chromosomes in the GnomAD database, including 2,092 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 0.16 (2092 hom., cov: 31)
• Consequence: LOC105377340 XR_001741771.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

LOC105377340 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377340	XR_001741771.2	n.633+1403C>T		intron_variant, non_coding_transcript_variant
LOC105377340	XR_939013.3	n.678C>T		non_coding_transcript_exon_variant	4/4
LOC105377340	XR_939014.2	n.191C>T		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24276 AN: 151870 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.160 AC: 24296 AN: 151990 Hom.: 2092 Cov.: 31 AF XY: 0.159 AC XY: 11796 AN XY: 74294

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.177

Alfa AF: 0.173 Hom.: 3662

Bravo AF: 0.159

Asia WGS AF: 0.305 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13134014; hg19: chr4-99104879;