chr16-85959043-C-T

Variant names:

• chr16-85959043-C-T
• rs12444486

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 0.555 in 151,650 control chromosomes in the GnomAD database, including 23,912 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 0.55 (23912 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.555 AC: 84059 AN: 151532 Hom.: 23915 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.555 AC: 84091 AN: 151650 Hom.: 23912 Cov.: 31 AF XY: 0.562 AC XY: 41620 AN XY: 74042

African (AFR) AF: 0.569 AC: 23537 AN: 41336

American (AMR) AF: 0.664 AC: 10138 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4314 AN: 5182

South Asian (SAS) AF: 0.660 AC: 3176 AN: 4812

European-Finnish (FIN) AF: 0.532 AC: 5544 AN: 10420

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33706 AN: 67860

Other (OTH) AF: 0.572 AC: 1203 AN: 2102

Alfa AF: 0.525 Hom.: 26188

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.89
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12444486; hg19: chr16-85992649;