rs224231

Variant names:

• chr16-3259979-C-T
• rs224231

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 0.51 in 151,380 control chromosomes in the GnomAD database, including 20,579 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 0.51 (20579 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.669 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: 0.509 AC: 77046 AN: 151262 Hom.: 20536 Cov.: 29

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.510 AC: 77148 AN: 151380 Hom.: 20579 Cov.: 29 AF XY: 0.509 AC XY: 37602 AN XY: 73892

African (AFR) AF: 0.675 AC: 27798 AN: 41170

American (AMR) AF: 0.516 AC: 7832 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1628 AN: 5116

South Asian (SAS) AF: 0.446 AC: 2140 AN: 4800

European-Finnish (FIN) AF: 0.452 AC: 4739 AN: 10478

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30109 AN: 67854

Other (OTH) AF: 0.486 AC: 1021 AN: 2100

Alfa AF: 0.486 Hom.: 2340

Bravo AF: 0.521

Asia WGS AF: 0.404 AC: 1409 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	1.5
DANN	Benign	0.61
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs224231; hg19: chr16-3309979;