rs3753580

Variant names:

• chr1-11860991-T-C
• rs3753580

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0361 in 147,788 control chromosomes in the GnomAD database, including 120 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 0.036 (120 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0361 (5336/147788) while in subpopulation NFE AF = 0.0484 (3258/67310). AF 95% confidence interval is 0.047. There are 120 homozygotes in GnomAd4. There are 2502 alleles in the male GnomAd4 subpopulation. Median coverage is 27. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 120 gene

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: 0.0361 AC: 5330 AN: 147672 Hom.: 120 Cov.: 27

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.0469

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0592

Gnomad EAS AF: 0.00725

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0325

Gnomad NFE AF: 0.0484

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0361 AC: 5336 AN: 147788 Hom.: 120 Cov.: 27 AF XY: 0.0348 AC XY: 2502 AN XY: 71800

African (AFR) AF: 0.0237 AC: 929 AN: 39230

American (AMR) AF: 0.0269 AC: 402 AN: 14926

Ashkenazi Jewish (ASJ) AF: 0.0592 AC: 204 AN: 3444

East Asian (EAS) AF: 0.00727 AC: 37 AN: 5090

South Asian (SAS) AF: 0.0473 AC: 219 AN: 4626

European-Finnish (FIN) AF: 0.0156 AC: 155 AN: 9922

Middle Eastern (MID) AF: 0.0382 AC: 11 AN: 288

European-Non Finnish (NFE) AF: 0.0484 AC: 3258 AN: 67310

Other (OTH) AF: 0.0384 AC: 79 AN: 2056

Alfa AF: 0.234 Hom.: 1249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.60
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3753580; hg19: chr1-11921048;