rs1775143

Variant names:

• chr1-205786422-C-T
• rs1775143

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 0.631 in 151,930 control chromosomes in the GnomAD database, including 32,411 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 0.63 (32411 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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: 0.632 AC: 95911 AN: 151812 Hom.: 32409 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.631 AC: 95936 AN: 151930 Hom.: 32411 Cov.: 31 AF XY: 0.631 AC XY: 46844 AN XY: 74272

African (AFR) AF: 0.395 AC: 16330 AN: 41378

American (AMR) AF: 0.560 AC: 8544 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2507 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2776 AN: 5170

South Asian (SAS) AF: 0.624 AC: 3004 AN: 4814

European-Finnish (FIN) AF: 0.796 AC: 8388 AN: 10538

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52116 AN: 67978

Other (OTH) AF: 0.663 AC: 1398 AN: 2108

Alfa AF: 0.637 Hom.: 11137

Bravo AF: 0.599

Asia WGS AF: 0.570 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.062
DANN	Benign	0.12
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1775143; hg19: chr1-205755550;