rs4417561

Variant names:

• chr16-79977462-C-G
• rs4417561

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 0.66 in 152,036 control chromosomes in the GnomAD database, including 33,562 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 0.66 (33562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.660 AC: 100281 AN: 151916 Hom.: 33544 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.660 AC: 100343 AN: 152036 Hom.: 33562 Cov.: 32 AF XY: 0.659 AC XY: 48940 AN XY: 74300

African (AFR) AF: 0.572 AC: 23715 AN: 41454

American (AMR) AF: 0.620 AC: 9464 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2649 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2736 AN: 5138

South Asian (SAS) AF: 0.689 AC: 3322 AN: 4820

European-Finnish (FIN) AF: 0.724 AC: 7659 AN: 10582

Middle Eastern (MID) AF: 0.693 AC: 201 AN: 290

European-Non Finnish (NFE) AF: 0.714 AC: 48548 AN: 67990

Other (OTH) AF: 0.671 AC: 1418 AN: 2112

Alfa AF: 0.691 Hom.: 4567

Bravo AF: 0.644

Asia WGS AF: 0.618 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4417561; hg19: chr16-80011359;