rs17781283

Positions:

• chr6-137941636-G-A

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 0.0204 in 152,120 control chromosomes in the GnomAD database, including 47 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 0.020 (47 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0204 (3102/152120) while in subpopulation NFE AF= 0.0311 (2116/67998). AF 95% confidence interval is 0.03. There are 47 homozygotes in gnomad4. There are 1415 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.137941636G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0204 AC: 3100 AN: 152002 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0204 AC: 3102 AN: 152120 Hom.: 47 Cov.: 33 AF XY: 0.0190 AC XY: 1415 AN XY: 74360

Gnomad4 AFR AF: 0.00569

Gnomad4 AMR AF: 0.0219

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0169

Gnomad4 NFE AF: 0.0311

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0254 Hom.: 12

Bravo AF: 0.0198

Asia WGS AF: 0.00462 AC: 16 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17781283; hg19: chr6-138262773;