16-27382270-T-C

Variant names:

• chr16-27382270-T-C
• rs9944340

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 0.29 in 152,114 control chromosomes in the GnomAD database, including 6,598 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 0.29 (6598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 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: 0.290 AC: 44055 AN: 151998 Hom.: 6587 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.290 AC: 44100 AN: 152114 Hom.: 6598 Cov.: 32 AF XY: 0.296 AC XY: 21987 AN XY: 74376

African (AFR) AF: 0.272 AC: 11288 AN: 41494

American (AMR) AF: 0.344 AC: 5260 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1887 AN: 5160

South Asian (SAS) AF: 0.409 AC: 1973 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3161 AN: 10580

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18740 AN: 67988

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.281 Hom.: 7840

Bravo AF: 0.291

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9944340; hg19: chr16-27393591;