rs1583977

chr4-99398605-T-A

Variant summary

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

The XR_939020.3(LOC102723576):n.1284+4228A>T 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 0.125 in 151,998 control chromosomes in the GnomAD database, including 1,205 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 0.12 (1205 hom., cov: 33)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1284+4228A>T		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.387+4228A>T		intron_variant, non_coding_transcript_variant
LOC102723576	XR_427569.4	n.1284+4228A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18904 AN: 151882 Hom.: 1198 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0456

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.125 AC: 18940 AN: 151998 Hom.: 1205 Cov.: 33 AF XY: 0.127 AC XY: 9400 AN XY: 74308

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0456

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.114

Alfa AF: 0.127 Hom.: 162

Bravo AF: 0.122

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1583977; hg19: chr4-100319762;