4-99383388-C-A

Position:

• chr4-99383388-C-A

Variant summary

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

The XR_939020.3(LOC102723576):​n.1413+104G>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 0.0995 in 150,788 control chromosomes in the GnomAD database, including 814 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 0.099 (814 hom., cov: 28)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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.1413+104G>T		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.620G>T		non_coding_transcript_exon_variant	4/4
LOC102723576	XR_427569.4	n.1517G>T		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 14989 AN: 150670 Hom.: 810 Cov.: 28

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0995 AC: 15003 AN: 150788 Hom.: 814 Cov.: 28 AF XY: 0.102 AC XY: 7502 AN XY: 73542

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0945 Hom.: 1022

Bravo AF: 0.0952

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372680; hg19: chr4-100304545;