chr3-135486509-C-T

Position:

• chr3-135486509-C-T

Variant summary

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

The XR_924528.4(LOC105374122):​n.732+5054G>A 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 0.153 in 152,204 control chromosomes in the GnomAD database, including 2,128 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 0.15 (2128 hom., cov: 33)
• Consequence: LOC105374122 XR_924528.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

Genes affected

LOC105374122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374122	XR_924528.4	n.732+5054G>A		intron_variant, non_coding_transcript_variant
LOC105374122	XR_001740926.1	n.735+5054G>A		intron_variant, non_coding_transcript_variant
LOC105374122	XR_007096111.1	n.735+5054G>A		intron_variant, non_coding_transcript_variant
LOC105374122	XR_924527.4	n.735+5054G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23291 AN: 152086 Hom.: 2125 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.153 AC: 23311 AN: 152204 Hom.: 2128 Cov.: 33 AF XY: 0.148 AC XY: 11031 AN XY: 74410

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.193

Alfa AF: 0.169 Hom.: 273

Bravo AF: 0.160

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs698267; hg19: chr3-135205351;