16-78071469-T-C

Variant names:

• chr16-78071469-T-C
• rs12925573

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 0.226 in 151,974 control chromosomes in the GnomAD database, including 4,757 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 0.23 (4757 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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: 0.226 AC: 34385 AN: 151856 Hom.: 4755 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.226 AC: 34375 AN: 151974 Hom.: 4757 Cov.: 31 AF XY: 0.228 AC XY: 16933 AN XY: 74256

African (AFR) AF: 0.0603 AC: 2499 AN: 41476

American (AMR) AF: 0.217 AC: 3317 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5168

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4808

European-Finnish (FIN) AF: 0.374 AC: 3932 AN: 10520

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20580 AN: 67944

Other (OTH) AF: 0.211 AC: 447 AN: 2114

Alfa AF: 0.260 Hom.: 958

Bravo AF: 0.209

Asia WGS AF: 0.186 AC: 647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12925573; hg19: chr16-78105366;