rs448261

chr4-176516966-G-A

Variant summary

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

The XR_007058376.1(LOC124900817):n.1158-3338G>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 0.586 in 151,056 control chromosomes in the GnomAD database, including 26,140 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 0.59 (26140 hom., cov: 29)
• Consequence: LOC124900817 XR_007058376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900817	XR_007058376.1	n.1158-3338G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88448 AN: 150938 Hom.: 26106 Cov.: 29

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.586 AC: 88534 AN: 151056 Hom.: 26140 Cov.: 29 AF XY: 0.585 AC XY: 43163 AN XY: 73744

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.596

Alfa AF: 0.601 Hom.: 4646

Bravo AF: 0.584

Asia WGS AF: 0.507 AC: 1759 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.20
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs448261; hg19: chr4-177438117;