16-7853607-T-C

Variant names:

• chr16-7853607-T-C
• rs12446289

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 0.164 in 152,150 control chromosomes in the GnomAD database, including 2,617 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 0.16 (2617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 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: 0.164 AC: 24952 AN: 152032 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.164 AC: 24966 AN: 152150 Hom.: 2617 Cov.: 32 AF XY: 0.170 AC XY: 12638 AN XY: 74380

African (AFR) AF: 0.0478 AC: 1986 AN: 41512

American (AMR) AF: 0.324 AC: 4945 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 578 AN: 3472

East Asian (EAS) AF: 0.0863 AC: 447 AN: 5180

South Asian (SAS) AF: 0.159 AC: 767 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13279 AN: 68002

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.153 Hom.: 1044

Bravo AF: 0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12446289; hg19: chr16-7903609;