rs548726

Variant names:

• chr1-5853561-T-C
• rs548726

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 0.74 in 152,170 control chromosomes in the GnomAD database, including 41,818 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 0.74 (41818 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.740 AC: 112500 AN: 152052 Hom.: 41767 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.740 AC: 112605 AN: 152170 Hom.: 41818 Cov.: 33 AF XY: 0.743 AC XY: 55291 AN XY: 74382

African (AFR) AF: 0.770 AC: 31965 AN: 41510

American (AMR) AF: 0.752 AC: 11513 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2369 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4610 AN: 5172

South Asian (SAS) AF: 0.674 AC: 3235 AN: 4800

European-Finnish (FIN) AF: 0.784 AC: 8309 AN: 10600

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48218 AN: 67994

Other (OTH) AF: 0.714 AC: 1508 AN: 2112

Alfa AF: 0.723 Hom.: 127486

Bravo AF: 0.742

Asia WGS AF: 0.750 AC: 2611 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	1.3
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs548726; hg19: chr1-5913621;