4-107553429-G-T

Variant names:

• chr4-107553429-G-T
• rs1514728
• XR_939059.3:n.131-6469C>A

Variant summary

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

The XR_939059.3(LOC105377358):​n.131-6469C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,670 control chromosomes in the GnomAD database, including 30,998 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 0.64 (30998 hom., cov: 33)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 1 publications found

Genes affected

LOC105377358 (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 (AFR) allele frequency at 95% confidence interval = 0.661 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: 0.638 AC: 96701 AN: 151552 Hom.: 30963 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.638 AC: 96782 AN: 151670 Hom.: 30998 Cov.: 33 AF XY: 0.636 AC XY: 47134 AN XY: 74122

African (AFR) AF: 0.667 AC: 27630 AN: 41408

American (AMR) AF: 0.621 AC: 9448 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2194 AN: 3458

East Asian (EAS) AF: 0.517 AC: 2648 AN: 5124

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 7002 AN: 10558

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43388 AN: 67770

Other (OTH) AF: 0.639 AC: 1350 AN: 2112

Alfa AF: 0.640 Hom.: 114667

Bravo AF: 0.639

Asia WGS AF: 0.484 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1514728; hg19: chr4-108474586;