rs3753580

Positions:

• chr1-11860991-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 120 gene

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: 0.0361 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

Gnomad4 AFR AF: 0.0237

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0592

Gnomad4 EAS AF: 0.00727

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0484

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.141 Hom.: 86

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753580; hg19: chr1-11921048;