rs547984

Variant names:

• chr1-237933586-A-C
• rs547984

Your query was ambiguous. Multiple possible variants found:

• chr1-237933586-A-C
• chr1-237933586-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.602 in 152,028 control chromosomes in the GnomAD database, including 27,801 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 0.60 (27801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 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: 0.602 AC: 91493 AN: 151910 Hom.: 27777 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.602 AC: 91565 AN: 152028 Hom.: 27801 Cov.: 32 AF XY: 0.604 AC XY: 44842 AN XY: 74288

African (AFR) AF: 0.692 AC: 28682 AN: 41470

American (AMR) AF: 0.563 AC: 8598 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2188 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2644 AN: 5166

South Asian (SAS) AF: 0.597 AC: 2877 AN: 4816

European-Finnish (FIN) AF: 0.583 AC: 6153 AN: 10554

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38426 AN: 67962

Other (OTH) AF: 0.605 AC: 1280 AN: 2114

Alfa AF: 0.572 Hom.: 104293

Bravo AF: 0.601

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs547984; hg19: chr1-238096886;