rs1348276

chr4-99404473-A-Cchr4-99404473-A-Gchr4-99404473-A-T

Variant summary

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

The XR_939020.3(LOC102723576):n.908T>G 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 0.458 in 151,934 control chromosomes in the GnomAD database, including 17,125 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 0.46 (17125 hom., cov: 32)
• Consequence: LOC102723576 XR_939020.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.908T>G		non_coding_transcript_exon_variant	1/5
LOC102723576	XR_427569.4	n.908T>G		non_coding_transcript_exon_variant	1/4
LOC102723576	XR_001741777.2	n.164-295T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69530 AN: 151816 Hom.: 17113 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.458 AC: 69587 AN: 151934 Hom.: 17125 Cov.: 32 AF XY: 0.456 AC XY: 33873 AN XY: 74272

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.419

Alfa AF: 0.384 Hom.: 11244

Bravo AF: 0.468

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348276; hg19: chr4-100325630;