4-99392905-C-T

Position:

• chr4-99392905-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.1285-9285G>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 0.248 in 151,768 control chromosomes in the GnomAD database, including 5,444 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 0.25 (5444 hom., cov: 32)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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 = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1285-9285G>A		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.388-9285G>A		intron_variant, non_coding_transcript_variant
LOC102723576	XR_427569.4	n.1285-9285G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37622 AN: 151650 Hom.: 5438 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.248 AC: 37652 AN: 151768 Hom.: 5444 Cov.: 32 AF XY: 0.255 AC XY: 18928 AN XY: 74170

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.233

Alfa AF: 0.221 Hom.: 509

Bravo AF: 0.247

Asia WGS AF: 0.467 AC: 1616 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
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: rs2032350; hg19: chr4-100314062;