rs120963

Variant names:

• chr16-23596749-A-G
• rs120963

Your query was ambiguous. Multiple possible variants found:

• chr16-23596749-A-G
• chr16-23596749-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.274 in 152,060 control chromosomes in the GnomAD database, including 6,518 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 0.27 (6518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.274 AC: 41602 AN: 151942 Hom.: 6479 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.274 AC: 41703 AN: 152060 Hom.: 6518 Cov.: 32 AF XY: 0.276 AC XY: 20545 AN XY: 74324

African (AFR) AF: 0.426 AC: 17660 AN: 41440

American (AMR) AF: 0.249 AC: 3798 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1611 AN: 5180

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2617 AN: 10548

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13070 AN: 68008

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.248 Hom.: 1396

Bravo AF: 0.281

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-1.5
PromoterAI		0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs120963; hg19: chr16-23608070;