rs16885575

chr6-54613961-G-Achr6-54613961-G-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 0.0999 in 152,060 control chromosomes in the GnomAD database, including 808 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 0.10 (808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 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: 0.0999 AC: 15181 AN: 151942 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0999 AC: 15198 AN: 152060 Hom.: 808 Cov.: 32 AF XY: 0.101 AC XY: 7488 AN XY: 74306

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.0389 Hom.: 30

Bravo AF: 0.0994

Asia WGS AF: 0.147 AC: 513 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	1.8
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16885575; hg19: chr6-54478759;