chr2-16439169-C-A

Variant names:

• chr2-16439169-C-A
• rs6753768

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 0.718 in 151,966 control chromosomes in the GnomAD database, including 39,682 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 0.72 (39682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.718 AC: 109070 AN: 151848 Hom.: 39652 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.718 AC: 109155 AN: 151966 Hom.: 39682 Cov.: 31 AF XY: 0.722 AC XY: 53621 AN XY: 74246

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.744

Alfa AF: 0.723 Hom.: 6325

Bravo AF: 0.715

Asia WGS AF: 0.873 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6753768; hg19: chr2-16620437;