4-181378514-A-T

Variant names:

• chr4-181378514-A-T
• rs9332473
• XR_001741489.2:n.313-573T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741489.2(LOC107986205):​n.313-573T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LOC107986205 XR_001741489.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 2 publications found

Genes affected

LOC107986205 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.468 AC: 19376 AN: 41426

American (AMR) AF: 0.571 AC: 8721 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2675 AN: 5160

South Asian (SAS) AF: 0.539 AC: 2599 AN: 4824

European-Finnish (FIN) AF: 0.541 AC: 5713 AN: 10554

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38591 AN: 67966

Other (OTH) AF: 0.553 AC: 1171 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9332473; hg19: chr4-182299667;