4-71597255-T-C

Variant names:

• chr4-71597255-T-C
• rs1453459
• XR_001741716.2:n.217-1133T>C

Variant summary

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

The XR_001741716.2(LOC107986285):​n.217-1133T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,122 control chromosomes in the GnomAD database, including 1,450 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 0.13 (1450 hom., cov: 31)
• Consequence: LOC107986285 XR_001741716.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 3 publications found

Genes affected

LOC107986285 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.135 AC: 20460 AN: 152004 Hom.: 1447 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0784

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20471 AN: 152122 Hom.: 1450 Cov.: 31 AF XY: 0.130 AC XY: 9705 AN XY: 74386

African (AFR) AF: 0.163 AC: 6771 AN: 41484

American (AMR) AF: 0.120 AC: 1840 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3466

East Asian (EAS) AF: 0.100 AC: 517 AN: 5162

South Asian (SAS) AF: 0.0830 AC: 400 AN: 4820

European-Finnish (FIN) AF: 0.0760 AC: 806 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9301 AN: 67990

Other (OTH) AF: 0.134 AC: 282 AN: 2108

Alfa AF: 0.111 Hom.: 408

Bravo AF: 0.142

Asia WGS AF: 0.122 AC: 422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.64
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1453459; hg19: chr4-72462972;