chr5-150570684-C-T

Position:

• chr5-150570684-C-T

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 0.0261 in 152,260 control chromosomes in the GnomAD database, including 99 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 0.026 (99 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0261 (3975/152260) while in subpopulation AMR AF= 0.0453 (693/15288). AF 95% confidence interval is 0.0425. There are 99 homozygotes in gnomad4. There are 1851 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 99 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150570684C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0261 AC: 3970 AN: 152142 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0261 AC: 3975 AN: 152260 Hom.: 99 Cov.: 32 AF XY: 0.0249 AC XY: 1851 AN XY: 74450

Gnomad4 AFR AF: 0.00628

Gnomad4 AMR AF: 0.0453

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0284 Hom.: 54

Bravo AF: 0.0266

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17657199; hg19: chr5-149950246;