rs1114626

chr5-21233428-A-Cchr5-21233428-A-Gchr5-21233428-A-T

Variant summary

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

The XR_007058710.1(LOC124900950):n.622+38287T>G 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 0.946 in 152,058 control chromosomes in the GnomAD database, including 68,351 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 0.95 (68351 hom., cov: 30)
• Consequence: LOC124900950 XR_007058710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LOC124900950 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900950	XR_007058710.1	n.622+38287T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143775 AN: 151940 Hom.: 68298 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.946 AC: 143882 AN: 152058 Hom.: 68351 Cov.: 30 AF XY: 0.947 AC XY: 70382 AN XY: 74328

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.946

Alfa AF: 0.954 Hom.: 10047

Bravo AF: 0.941

Asia WGS AF: 0.887 AC: 3083 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	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1114626; hg19: chr5-21233537;