rs11134178

Positions:

• chr5-6834054-T-C

Variant summary

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

The XR_925740.3(LOC105374641):​n.1189T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 152,306 control chromosomes in the GnomAD database, including 130 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 0.037 (130 hom., cov: 33)
• Consequence: LOC105374641 XR_925740.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

LOC105374641 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374641	XR_925740.3	n.1189T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 5683 AN: 152188 Hom.: 129 Cov.: 33

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0373 AC: 5686 AN: 152306 Hom.: 130 Cov.: 33 AF XY: 0.0364 AC XY: 2710 AN XY: 74490

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0523

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0533 Hom.: 282

Bravo AF: 0.0357

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11134178; hg19: chr5-6834167;