rs7539281

Variant names:

• chr1-162038244-G-A
• rs7539281

Your query was ambiguous. Multiple possible variants found:

• chr1-162038244-G-A
• chr1-162038244-G-C

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 0.375 in 152,076 control chromosomes in the GnomAD database, including 12,568 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 0.38 (12568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.375 AC: 57012 AN: 151958 Hom.: 12541 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.375 AC: 57088 AN: 152076 Hom.: 12568 Cov.: 32 AF XY: 0.378 AC XY: 28086 AN XY: 74350

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.369

Alfa AF: 0.282 Hom.: 12923

Bravo AF: 0.380

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.93
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7539281; hg19: chr1-162008034;