rs2126736

Positions:

• chr5-75279159-A-G

Variant summary

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

The XR_007058824.1(LOC124901007):​n.182-3654T>C 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 0.494 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

LOC124901007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901007	XR_007058824.1	n.182-3654T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.495

Alfa AF: 0.437 Hom.: 25989

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2126736; hg19: chr5-74574984;