rs2038037

Positions:

• chr6-16175064-A-G
• chr6-16175064-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.595 in 151,946 control chromosomes in the GnomAD database, including 29,775 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 0.60 (29775 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16175064A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90325 AN: 151828 Hom.: 29714 Cov.: 30

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.595 AC: 90446 AN: 151946 Hom.: 29775 Cov.: 30 AF XY: 0.593 AC XY: 44053 AN XY: 74298

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.550

Alfa AF: 0.479 Hom.: 23722

Bravo AF: 0.627

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038037; hg19: chr6-16175295;