rs1330387

Variant names:

• chr1-170117885-A-G
• rs1330387

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 0.0332 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 96 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0280 AC: 1162 AN: 41574

American (AMR) AF: 0.0188 AC: 288 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3470

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5192

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4828

European-Finnish (FIN) AF: 0.0303 AC: 322 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0414 AC: 2814 AN: 68026

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.68
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1330387;

hg19: chr1-170087026;