rs4823568

chr22-46142032-A-T

Variant summary

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

The XR_007068140.1(LOC124905138):n.804-887T>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 0.235 in 119,590 control chromosomes in the GnomAD database, including 3,430 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 0.24 (3430 hom., cov: 18)
• Consequence: LOC124905138 XR_007068140.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

Genes affected

LOC124905138 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905138	XR_007068140.1	n.804-887T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 28119 AN: 119620 Hom.: 3430 Cov.: 18

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.235 AC: 28112 AN: 119590 Hom.: 3430 Cov.: 18 AF XY: 0.230 AC XY: 13008 AN XY: 56610

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.205

Alfa AF: 0.0707 Hom.: 92

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.3
Dann	Benign	0.054

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4823568; hg19: chr22-46537906;