rs1032296

chr4-144513536-T-C

Variant summary

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

The XR_939273.3(LOC105377462):n.164+48448A>G 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 0.683 in 152,086 control chromosomes in the GnomAD database, including 36,473 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 0.68 (36473 hom., cov: 33)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.164+48448A>G		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.165-14016A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103708 AN: 151968 Hom.: 36425 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.683 AC: 103819 AN: 152086 Hom.: 36473 Cov.: 33 AF XY: 0.687 AC XY: 51086 AN XY: 74340

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.633

Alfa AF: 0.612 Hom.: 27236

Bravo AF: 0.677

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1032296; hg19: chr4-145434688;