rs1368350

Positions:

• chr5-145851487-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 0.024 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.145851487A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.00474

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00934

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0256

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368350; hg19: chr5-145231050;