4-159577814-G-T

Variant names:

• chr4-159577814-G-T
• rs1354252
• XR_001741911.2:n.76+37416G>T

Variant summary

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

The XR_001741911.2(LOC107986324):​n.76+37416G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,020 control chromosomes in the GnomAD database, including 6,478 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 0.25 (6478 hom., cov: 31)
• Consequence: LOC107986324 XR_001741911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 1 publications found

Genes affected

LOC107986324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.245 AC: 37208 AN: 151902 Hom.: 6445 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.245 AC: 37294 AN: 152020 Hom.: 6478 Cov.: 31 AF XY: 0.238 AC XY: 17716 AN XY: 74330

African (AFR) AF: 0.493 AC: 20421 AN: 41434

American (AMR) AF: 0.159 AC: 2423 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5178

South Asian (SAS) AF: 0.179 AC: 864 AN: 4820

European-Finnish (FIN) AF: 0.0931 AC: 985 AN: 10576

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11190 AN: 67964

Other (OTH) AF: 0.220 AC: 462 AN: 2104

Alfa AF: 0.200 Hom.: 989

Bravo AF: 0.257

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1354252; hg19: chr4-160498966;