chr5-75279159-A-G

Variant names:

• chr5-75279159-A-G
• rs2126736
• XR_007058824.1:n.182-3654T>C

Variant summary

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

The XR_007058824.1(LOC124901007):​n.182-3654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,034 control chromosomes in the GnomAD database, including 19,075 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 0.49 (19075 hom., cov: 32)
• Consequence: LOC124901007 XR_007058824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

Genes affected

LOC124901007 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901007	XR_007058824.1	n.182-3654T>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74956 AN: 151916 Hom.: 19044 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.494 AC: 75050 AN: 152034 Hom.: 19075 Cov.: 32 AF XY: 0.497 AC XY: 36930 AN XY: 74312

African (AFR) AF: 0.616 AC: 25525 AN: 41428

American (AMR) AF: 0.464 AC: 7096 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2885 AN: 5180

South Asian (SAS) AF: 0.599 AC: 2891 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4748 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28584 AN: 67978

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.448 Hom.: 61289

Bravo AF: 0.497

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2126736; hg19: chr5-74574984;