rs2274509

chr1-182589381-A-G

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 0.36 in 152,050 control chromosomes in the GnomAD database, including 9,943 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 0.36 (9942 hom., cov: 32)
  • Exomes 𝑓: 0.32 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54642 AN: 151904 Hom.: 9941 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.351

GnomAD4 exome AF: 0.321 AC: 9 AN: 28 Hom.: 1 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.318

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.360 AC: 54661 AN: 152022 Hom.: 9942 Cov.: 32 AF XY: 0.357 AC XY: 26542 AN XY: 74288

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.352

Alfa AF: 0.372 Hom.: 2781

Bravo AF: 0.348

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.2
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2274509; hg19: chr1-182558516;