rs1501241

Variant names:

• chr1-60424002-G-A
• rs1501241

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 0.0685 in 151,966 control chromosomes in the GnomAD database, including 1,004 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 0.069 (1004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10390 AN: 151850 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.00924

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.00322

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00615

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0685 AC: 10410 AN: 151966 Hom.: 1004 Cov.: 32 AF XY: 0.0681 AC XY: 5057 AN XY: 74284

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.00924

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.00322

Gnomad4 NFE AF: 0.00615

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0301 Hom.: 117

Bravo AF: 0.0764

Asia WGS AF: 0.0780 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1501241; hg19: chr1-60889674;