rs546785

chr1-175748332-A-Cchr1-175748332-A-T

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 0.658 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.681

Alfa AF: 0.695 Hom.: 50498

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs546785; hg19: chr1-175717468;