rs2386817

Variant names:

• chr16-3888601-T-A
• rs2386817

Your query was ambiguous. Multiple possible variants found:

• chr16-3888601-T-A
• chr16-3888601-T-C
• chr16-3888601-T-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 0.848 in 152,144 control chromosomes in the GnomAD database, including 57,409 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 0.85 (57409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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: 0.849 AC: 129047 AN: 152026 Hom.: 57399 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.848 AC: 129084 AN: 152144 Hom.: 57409 Cov.: 31 AF XY: 0.851 AC XY: 63295 AN XY: 74380

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.868

Alfa AF: 0.906 Hom.: 7990

Bravo AF: 0.830

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2386817; hg19: chr16-3938602;