rs1646332

Variant names:

• chr16-13955870-C-A
• rs1646332

Your query was ambiguous. Multiple possible variants found:

• chr16-13955870-C-A
• chr16-13955870-C-G
• chr16-13955870-C-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 0.382 in 152,034 control chromosomes in the GnomAD database, including 11,875 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 0.38 (11875 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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: 0.381 AC: 57925 AN: 151916 Hom.: 11841 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.382 AC: 58017 AN: 152034 Hom.: 11875 Cov.: 33 AF XY: 0.377 AC XY: 28003 AN XY: 74340

African (AFR) AF: 0.528 AC: 21882 AN: 41438

American (AMR) AF: 0.288 AC: 4407 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1274 AN: 5168

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4824

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10564

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23247 AN: 67976

Other (OTH) AF: 0.389 AC: 823 AN: 2114

Alfa AF: 0.336 Hom.: 4866

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.21
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1646332; hg19: chr16-14049727;