rs318218

chr16-64223641-G-Achr16-64223641-G-C

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 0.0767 in 152,152 control chromosomes in the GnomAD database, including 515 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 0.077 (515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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 = 0.0988 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: 0.0768 AC: 11674 AN: 152034 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0767 AC: 11677 AN: 152152 Hom.: 515 Cov.: 32 AF XY: 0.0736 AC XY: 5478 AN XY: 74396

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.0672

Gnomad4 SAS AF: 0.0615

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0221 Hom.: 13

Bravo AF: 0.0762

Asia WGS AF: 0.0760 AC: 266 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	0.087
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs318218; hg19: chr16-64257545;