rs1442484

chr4-99385019-T-Cchr4-99385019-T-G

Variant summary

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

The XR_939020.3(LOC102723576):n.1285-1399A>G 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 0.25 in 151,998 control chromosomes in the GnomAD database, including 5,546 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 (5546 hom., cov: 32)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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 = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1285-1399A>G		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.388-1399A>G		intron_variant, non_coding_transcript_variant
LOC102723576	XR_427569.4	n.1285-1399A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37923 AN: 151880 Hom.: 5539 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.250 AC: 37957 AN: 151998 Hom.: 5546 Cov.: 32 AF XY: 0.257 AC XY: 19059 AN XY: 74280

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.236

Alfa AF: 0.102 Hom.: 154

Bravo AF: 0.250

Asia WGS AF: 0.468 AC: 1625 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.87
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1442484; hg19: chr4-100306176;