6-16175064-A-G

Variant names:

• chr6-16175064-A-G
• rs2038037

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;