4-159567154-G-T

Variant names:

• chr4-159567154-G-T
• rs9992703
• XR_001741911.2:n.76+26756G>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+26756G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,888 control chromosomes in the GnomAD database, including 16,132 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 0.45 (16132 hom., cov: 31)
• Consequence: LOC107986324 XR_001741911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.452 AC: 68620 AN: 151770 Hom.: 16114 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.452 AC: 68686 AN: 151888 Hom.: 16132 Cov.: 31 AF XY: 0.458 AC XY: 34017 AN XY: 74230

African (AFR) AF: 0.435 AC: 18010 AN: 41410

American (AMR) AF: 0.590 AC: 8999 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3681 AN: 5162

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4831 AN: 10558

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.414 AC: 28146 AN: 67920

Other (OTH) AF: 0.465 AC: 982 AN: 2110

Alfa AF: 0.437 Hom.: 2205

Bravo AF: 0.465

Asia WGS AF: 0.547 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.31
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs9992703; hg19: chr4-160488306;