chr16-55221279-T-C

Variant names:

• chr16-55221279-T-C
• rs2001970

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 0.485 in 151,952 control chromosomes in the GnomAD database, including 18,140 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 0.48 (18140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.485 AC: 73650 AN: 151834 Hom.: 18133 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.485 AC: 73696 AN: 151952 Hom.: 18140 Cov.: 32 AF XY: 0.488 AC XY: 36250 AN XY: 74272

African (AFR) AF: 0.436 AC: 18042 AN: 41398

American (AMR) AF: 0.465 AC: 7105 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2011 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3515 AN: 5164

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5413 AN: 10560

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32863 AN: 67950

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.488 Hom.: 38031

Bravo AF: 0.482

Asia WGS AF: 0.633 AC: 2204 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	0.43
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2001970; hg19: chr16-55255191;