rs1330387

chr1-170117885-A-G

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 0.0332 in 152,336 control chromosomes in the GnomAD database, including 96 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 0.033 (96 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0332 (5056/152336) while in subpopulation SAS AF= 0.0468 (226/4828). AF 95% confidence interval is 0.0418. There are 96 homozygotes in gnomad4. There are 2338 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 96 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: 0.0331 AC: 5040 AN: 152218 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0332 AC: 5056 AN: 152336 Hom.: 96 Cov.: 32 AF XY: 0.0314 AC XY: 2338 AN XY: 74508

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0468

Gnomad4 FIN AF: 0.0303

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0350 Hom.: 20

Bravo AF: 0.0315

Asia WGS AF: 0.0430 AC: 151 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330387; hg19: chr1-170087026;