rs1441302

Variant names:

• chr4-60157175-G-A
• rs1441302

Your query was ambiguous. Multiple possible variants found:

• chr4-60157175-G-A
• chr4-60157175-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 0.0637 in 151,966 control chromosomes in the GnomAD database, including 432 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 (432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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: 0.0636 AC: 9657 AN: 151848 Hom.: 425 Cov.: 31

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0637 AC: 9676 AN: 151966 Hom.: 432 Cov.: 31 AF XY: 0.0673 AC XY: 4997 AN XY: 74266

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0608

Gnomad4 OTH AF: 0.0721

Alfa AF: 0.0687 Hom.: 202

Bravo AF: 0.0601

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1441302; hg19: chr4-61022893;