rs1018910

Positions:

• chr16-71244565-A-G
• chr16-71244565-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 0.326 in 152,086 control chromosomes in the GnomAD database, including 8,877 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 0.33 (8877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

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 (AMR) allele frequency at 95% confidence interval = 0.447 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: 0.326 AC: 49560 AN: 151968 Hom.: 8840 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.326 AC: 49652 AN: 152086 Hom.: 8877 Cov.: 32 AF XY: 0.325 AC XY: 24135 AN XY: 74346

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.316

Alfa AF: 0.310 Hom.: 1404

Bravo AF: 0.353

Asia WGS AF: 0.289 AC: 1005 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	9.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018910; hg19: chr16-71278468;