rs2486746

Positions:

• chr1-231361578-G-A

Variant summary

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

The variant allele was found at a frequency of 0.577 in 151,534 control chromosomes in the GnomAD database, including 26,015 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 0.58 (26015 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.231361578G>A		intergenic_region
LOC107985360	XR_001738520.3	n.4098+191G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87378 AN: 151416 Hom.: 26002 Cov.: 28

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.577 AC: 87426 AN: 151534 Hom.: 26015 Cov.: 28 AF XY: 0.581 AC XY: 42963 AN XY: 74002

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.590

Alfa AF: 0.583 Hom.: 4962

Bravo AF: 0.559

Asia WGS AF: 0.569 AC: 1977 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	0.022
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486746; hg19: chr1-231497324; COSMIC: COSV64148217;