chr4-181406790-A-G

Variant names:

• chr4-181406790-A-G
• rs724659
• XR_007058402.1:n.78-12216T>C

Variant summary

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

The XR_007058402.1(LOC124900822):​n.78-12216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,036 control chromosomes in the GnomAD database, including 12,778 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 0.40 (12778 hom., cov: 33)
• Consequence: LOC124900822 XR_007058402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 5 publications found

Genes affected

LOC124900822 (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 (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.404 AC: 61420 AN: 151920 Hom.: 12773 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.404 AC: 61458 AN: 152036 Hom.: 12778 Cov.: 33 AF XY: 0.400 AC XY: 29750 AN XY: 74292

African (AFR) AF: 0.337 AC: 13980 AN: 41490

American (AMR) AF: 0.383 AC: 5851 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1508 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1231 AN: 5162

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4773 AN: 10552

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31136 AN: 67952

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.440 Hom.: 25581

Bravo AF: 0.395

Asia WGS AF: 0.279 AC: 973 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	0.43
DANN	Benign	0.44
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs724659; hg19: chr4-182327943;