4-180410693-A-T

Variant names:

• chr4-180410693-A-T
• rs2309248
• XR_001741469.2:n.1399+10208A>T

Variant summary

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

The XR_001741469.2(LOC105377567):​n.1399+10208A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,900 control chromosomes in the GnomAD database, including 24,823 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 0.56 (24823 hom., cov: 32)
• Consequence: LOC105377567 XR_001741469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

LOC105377567 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85261 AN: 151782 Hom.: 24817 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.562 AC: 85315 AN: 151900 Hom.: 24823 Cov.: 32 AF XY: 0.554 AC XY: 41090 AN XY: 74206

African (AFR) AF: 0.412 AC: 17067 AN: 41450

American (AMR) AF: 0.582 AC: 8878 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3468

East Asian (EAS) AF: 0.656 AC: 3373 AN: 5138

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4820

European-Finnish (FIN) AF: 0.512 AC: 5403 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43518 AN: 67908

Other (OTH) AF: 0.604 AC: 1274 AN: 2108

Alfa AF: 0.505 Hom.: 1588

Bravo AF: 0.561

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2309248; hg19: chr4-181331846;