chr1-248333561-A-G

Variant names:

• chr1-248333561-A-G
• rs4481887

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 0.799 in 152,170 control chromosomes in the GnomAD database, including 49,035 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 0.80 (49035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.799 AC: 121546 AN: 152052 Hom.: 48992 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.799 AC: 121647 AN: 152170 Hom.: 49035 Cov.: 32 AF XY: 0.804 AC XY: 59784 AN XY: 74404

African (AFR) AF: 0.883 AC: 36657 AN: 41518

American (AMR) AF: 0.791 AC: 12098 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3468

East Asian (EAS) AF: 0.861 AC: 4450 AN: 5170

South Asian (SAS) AF: 0.878 AC: 4235 AN: 4826

European-Finnish (FIN) AF: 0.804 AC: 8516 AN: 10588

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50607 AN: 67994

Other (OTH) AF: 0.775 AC: 1638 AN: 2114

Alfa AF: 0.756 Hom.: 194200

Bravo AF: 0.800

Asia WGS AF: 0.864 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.26
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4481887; hg19: chr1-248496863;