chr4-180122242-G-A

Variant names:

• chr4-180122242-G-A
• rs1447338
• XR_007058392.1:n.22637G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007058392.1(LOC124900623):​n.22637G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,634 control chromosomes in the GnomAD database, including 33,924 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 0.63 (33924 hom., cov: 31)
• Consequence: LOC124900623 XR_007058392.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 5 publications found

Genes affected

LOC124900623 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900623	XR_007058392.1	n.22637G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307510	ENST00000826655.1	n.75-26573G>A		intron_variant	Intron 1 of 2
ENSG00000307510	ENST00000826656.1	n.40-26573G>A		intron_variant	Intron 1 of 3
ENSG00000307510	ENST00000826657.1	n.34-26573G>A		intron_variant	Intron 1 of 3
ENSG00000307510	ENST00000826658.1	n.52-26573G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95103 AN: 151516 Hom.: 33915 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.627 AC: 95131 AN: 151634 Hom.: 33924 Cov.: 31 AF XY: 0.635 AC XY: 47026 AN XY: 74096

African (AFR) AF: 0.267 AC: 11053 AN: 41390

American (AMR) AF: 0.717 AC: 10872 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2380 AN: 3444

East Asian (EAS) AF: 0.895 AC: 4605 AN: 5148

South Asian (SAS) AF: 0.795 AC: 3814 AN: 4800

European-Finnish (FIN) AF: 0.785 AC: 8274 AN: 10546

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52026 AN: 67840

Other (OTH) AF: 0.640 AC: 1344 AN: 2100

Alfa AF: 0.717 Hom.: 8337

Bravo AF: 0.604

Asia WGS AF: 0.790 AC: 2743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	15
DANN	Benign	0.60
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1447338; hg19: chr4-181043395;