rs1368350

Variant names:

• chr5-145851487-A-G
• rs1368350

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 0.024 in 152,204 control chromosomes in the GnomAD database, including 65 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 0.024 (65 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.024 (3648/152204) while in subpopulation NFE AF = 0.0313 (2126/68014). AF 95% confidence interval is 0.0302. There are 65 homozygotes in GnomAd4. There are 1856 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0240 AC: 3649 AN: 152086 Hom.: 65 Cov.: 32

Gnomad AFR AF: 0.00476

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00933

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0240 AC: 3648 AN: 152204 Hom.: 65 Cov.: 32 AF XY: 0.0249 AC XY: 1856 AN XY: 74394

African (AFR) AF: 0.00474 AC: 197 AN: 41534

American (AMR) AF: 0.0231 AC: 354 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.00934 AC: 45 AN: 4820

European-Finnish (FIN) AF: 0.0591 AC: 625 AN: 10580

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0313 AC: 2126 AN: 68014

Other (OTH) AF: 0.0256 AC: 54 AN: 2110

Alfa AF: 0.0288 Hom.: 7

Bravo AF: 0.0215

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.6
DANN	Benign	0.65
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs1368350; hg19: chr5-145231050;