rs1495244

Positions:

• chr1-4282544-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 0.374 in 151,960 control chromosomes in the GnomAD database, including 12,884 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 0.37 (12884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56815 AN: 151842 Hom.: 12846 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.374 AC: 56908 AN: 151960 Hom.: 12884 Cov.: 32 AF XY: 0.375 AC XY: 27842 AN XY: 74274

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.345

Alfa AF: 0.282 Hom.: 6652

Bravo AF: 0.383

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1495244; hg19: chr1-4342604;