chr16-86120749-G-C

Variant names:

• chr16-86120749-G-C
• rs9941308

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 0.323 in 150,322 control chromosomes in the GnomAD database, including 8,388 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 0.32 (8388 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.362 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: 0.323 AC: 48518 AN: 150204 Hom.: 8384 Cov.: 29

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.323 AC: 48539 AN: 150322 Hom.: 8388 Cov.: 29 AF XY: 0.317 AC XY: 23280 AN XY: 73374

African (AFR) AF: 0.297 AC: 12178 AN: 40952

American (AMR) AF: 0.267 AC: 4027 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1561 AN: 3440

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5162

South Asian (SAS) AF: 0.327 AC: 1555 AN: 4760

European-Finnish (FIN) AF: 0.320 AC: 3299 AN: 10306

Middle Eastern (MID) AF: 0.486 AC: 140 AN: 288

European-Non Finnish (NFE) AF: 0.366 AC: 24613 AN: 67328

Other (OTH) AF: 0.355 AC: 741 AN: 2090

Alfa AF: 0.347 Hom.: 1178

Bravo AF: 0.320

Asia WGS AF: 0.192 AC: 663 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.25
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9941308; hg19: chr16-86154355;