4-180920041-C-T

Variant names:

• chr4-180920041-C-T
• rs1969398
• XR_007058399.1:n.206-860G>A

Variant summary

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

The XR_007058399.1(LOC124900821):​n.206-860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 151,986 control chromosomes in the GnomAD database, including 62,284 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 0.90 (62284 hom., cov: 34)
• Consequence: LOC124900821 XR_007058399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 1 publications found

Genes affected

LOC124900821 (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 (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.903 AC: 137176 AN: 151870 Hom.: 62254 Cov.: 34

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.903 AC: 137256 AN: 151986 Hom.: 62284 Cov.: 34 AF XY: 0.908 AC XY: 67458 AN XY: 74328

African (AFR) AF: 0.785 AC: 32409 AN: 41260

American (AMR) AF: 0.943 AC: 14421 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5163 AN: 5182

South Asian (SAS) AF: 0.971 AC: 4689 AN: 4828

European-Finnish (FIN) AF: 0.966 AC: 10257 AN: 10618

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63794 AN: 68006

Other (OTH) AF: 0.932 AC: 1973 AN: 2116

Alfa AF: 0.904 Hom.: 3312

Bravo AF: 0.901

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1969398; hg19: chr4-181841194;