rs16871226

chr6-32948074-A-G

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 0.0368 in 152,302 control chromosomes in the GnomAD database, including 136 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 0.037 (136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5606 AN: 152184 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0368 AC: 5610 AN: 152302 Hom.: 136 Cov.: 32 AF XY: 0.0352 AC XY: 2624 AN XY: 74478

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0689

Gnomad4 SAS AF: 0.0248

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0324 Hom.: 159

Bravo AF: 0.0424

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.71
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16871226; hg19: chr6-32915851;