4-181406790-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900822	XR_007058402.1	n.78-12216T>C		intron_variant	Intron 1 of 3

Ensembl

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

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 v4.3

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;