rs724658

Variant names:

• chr4-181406685-C-A
• rs724658
• XR_007058402.1:n.78-12111G>T

Variant summary

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

The XR_007058402.1(LOC124900822):​n.78-12111G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,074 control chromosomes in the GnomAD database, including 3,019 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 0.19 (3019 hom., cov: 32)
• Consequence: LOC124900822 XR_007058402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900822	XR_007058402.1	n.78-12111G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28304 AN: 151954 Hom.: 3017 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.186 AC: 28304 AN: 152074 Hom.: 3019 Cov.: 32 AF XY: 0.191 AC XY: 14220 AN XY: 74334

African (AFR) AF: 0.0780 AC: 3239 AN: 41506

American (AMR) AF: 0.247 AC: 3772 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1479 AN: 5158

South Asian (SAS) AF: 0.258 AC: 1238 AN: 4806

European-Finnish (FIN) AF: 0.250 AC: 2643 AN: 10554

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14601 AN: 67988

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.205 Hom.: 5783

Bravo AF: 0.181

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs724658; hg19: chr4-182327838;