rs1441301

Variant names:

• chr4-60157110-G-A
• rs1441301

Your query was ambiguous. Multiple possible variants found:

• chr4-60157110-G-A
• chr4-60157110-G-T

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 0.0641 in 151,864 control chromosomes in the GnomAD database, including 441 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 0.064 (441 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.0641 AC: 9727 AN: 151746 Hom.: 437 Cov.: 31

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0641 AC: 9734 AN: 151864 Hom.: 441 Cov.: 31 AF XY: 0.0678 AC XY: 5032 AN XY: 74170

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0602 Hom.: 175

Bravo AF: 0.0599

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
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: rs1441301; hg19: chr4-61022828;