rs724658

Positions:

• chr4-181406685-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058402.1(LOC124900822):​n.78-12111G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

LOC124900822 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124900822	XR_007058402.1	n.78-12111G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0780

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.192

Alfa AF: 0.208 Hom.: 4601

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724658; hg19: chr4-182327838;