rs7186128

Positions:

• chr16-16864058-G-A

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 0.701 in 150,160 control chromosomes in the GnomAD database, including 36,965 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 0.70 (36965 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.701 AC: 105191 AN: 150058 Hom.: 36937 Cov.: 27

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.701 AC: 105268 AN: 150160 Hom.: 36965 Cov.: 27 AF XY: 0.696 AC XY: 50866 AN XY: 73104

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.703

Alfa AF: 0.699 Hom.: 25516

Bravo AF: 0.704

Asia WGS AF: 0.708 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7186128; hg19: chr16-16957915;