rs9332473

Positions:

• chr4-181378514-A-T

Variant summary

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

The variant allele was found at a frequency of 0.537 in 151,994 control chromosomes in the GnomAD database, including 22,002 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 0.54 (22002 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.181378514A>T		intergenic_region
LOC107986205	XR_001741489.2	n.313-573T>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81611 AN: 151876 Hom.: 21986 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.537 AC: 81661 AN: 151994 Hom.: 22002 Cov.: 32 AF XY: 0.537 AC XY: 39917 AN XY: 74272

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.553

Alfa AF: 0.556 Hom.: 2918

Bravo AF: 0.536

Asia WGS AF: 0.548 AC: 1902 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332473; hg19: chr4-182299667;