rs546785

Variant names:

• chr1-175748332-A-C
• rs546785

Your query was ambiguous. Multiple possible variants found:

• chr1-175748332-A-C
• chr1-175748332-A-T

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 0.658 in 151,946 control chromosomes in the GnomAD database, including 33,752 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 0.66 (33752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 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: 0.659 AC: 99998 AN: 151828 Hom.: 33727 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.658 AC: 100054 AN: 151946 Hom.: 33752 Cov.: 31 AF XY: 0.665 AC XY: 49399 AN XY: 74290

African (AFR) AF: 0.497 AC: 20598 AN: 41418

American (AMR) AF: 0.745 AC: 11382 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2422 AN: 3462

East Asian (EAS) AF: 0.729 AC: 3760 AN: 5156

South Asian (SAS) AF: 0.805 AC: 3878 AN: 4816

European-Finnish (FIN) AF: 0.756 AC: 7983 AN: 10560

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47780 AN: 67954

Other (OTH) AF: 0.681 AC: 1431 AN: 2100

Alfa AF: 0.693 Hom.: 59753

Bravo AF: 0.647

Asia WGS AF: 0.767 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs546785; hg19: chr1-175717468;