rs1372679

chr4-99383373-C-T

Variant summary

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

The XR_939020.3(LOC102723576):n.1413+119G>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 0.0907 in 150,956 control chromosomes in the GnomAD database, including 717 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 0.091 (717 hom., cov: 28)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1413+119G>A		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.635G>A		non_coding_transcript_exon_variant	4/4
LOC102723576	XR_427569.4	n.1532G>A		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 13689 AN: 150840 Hom.: 714 Cov.: 28

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0335

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0907 AC: 13698 AN: 150956 Hom.: 717 Cov.: 28 AF XY: 0.0934 AC XY: 6878 AN XY: 73650

Gnomad4 AFR AF: 0.0464

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.0335

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0991 Hom.: 419

Bravo AF: 0.0850

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.45
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372679; hg19: chr4-100304530;