rs1530044

Positions:

• chr4-165506259-T-A

Variant summary

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

The XR_939419.2(LOC105377520):​n.233+126T>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 0.311 in 152,154 control chromosomes in the GnomAD database, including 13,063 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 0.31 (13063 hom., cov: 33)
• Consequence: LOC105377520 XR_939419.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

Genes affected

LOC105377520 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377520	XR_939419.2	n.233+126T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47256 AN: 152036 Hom.: 13016 Cov.: 33

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.311 AC: 47356 AN: 152154 Hom.: 13063 Cov.: 33 AF XY: 0.306 AC XY: 22782 AN XY: 74406

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.241

Alfa AF: 0.235 Hom.: 1027

Bravo AF: 0.332

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1530044; hg19: chr4-166427411;