16-9249490-G-A

Variant names:

• chr16-9249490-G-A
• rs1397142

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 0.383 in 151,924 control chromosomes in the GnomAD database, including 11,336 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 0.38 (11336 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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: 0.383 AC: 58183 AN: 151806 Hom.: 11331 Cov.: 30

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.383 AC: 58227 AN: 151924 Hom.: 11336 Cov.: 30 AF XY: 0.380 AC XY: 28213 AN XY: 74274

African (AFR) AF: 0.392 AC: 16257 AN: 41420

American (AMR) AF: 0.373 AC: 5693 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2169 AN: 5156

South Asian (SAS) AF: 0.371 AC: 1781 AN: 4796

European-Finnish (FIN) AF: 0.313 AC: 3296 AN: 10546

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26305 AN: 67950

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.383 Hom.: 10224

Bravo AF: 0.391

Asia WGS AF: 0.415 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.016
DANN	Benign	0.81
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1397142; hg19: chr16-9343347;