16-61448912-T-C

Variant names:

• chr16-61448912-T-C
• rs1550823

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 0.571 in 151,980 control chromosomes in the GnomAD database, including 24,938 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 0.57 (24938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.571 AC: 86661 AN: 151862 Hom.: 24914 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.571 AC: 86732 AN: 151980 Hom.: 24938 Cov.: 31 AF XY: 0.563 AC XY: 41818 AN XY: 74290

African (AFR) AF: 0.581 AC: 24086 AN: 41438

American (AMR) AF: 0.535 AC: 8169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3466

East Asian (EAS) AF: 0.534 AC: 2746 AN: 5142

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4814

European-Finnish (FIN) AF: 0.475 AC: 5027 AN: 10576

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40332 AN: 67960

Other (OTH) AF: 0.591 AC: 1242 AN: 2102

Alfa AF: 0.578 Hom.: 11834

Bravo AF: 0.578

Asia WGS AF: 0.463 AC: 1607 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.48
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1550823; hg19: chr16-61482816;