XR_007067617.1:n.148+1587A>G

Variant names:

• chr20-46769636-T-C
• rs3091430
• XR_007067617.1:n.148+1587A>G

Variant summary

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

The XR_007067617.1(LOC124904919):​n.148+1587A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,186 control chromosomes in the GnomAD database, including 7,972 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 0.29 (7972 hom., cov: 32)
• Consequence: LOC124904919 XR_007067617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

LOC124904919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904919	XR_007067617.1	n.148+1587A>G		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43416 AN: 152068 Hom.: 7957 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.286 AC: 43453 AN: 152186 Hom.: 7972 Cov.: 32 AF XY: 0.299 AC XY: 22257 AN XY: 74404

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.333

Alfa AF: 0.283 Hom.: 855

Bravo AF: 0.285

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091430; hg19: chr20-45398275;