rs16850408

Positions:

• chr4-74067090-C-A
• chr4-74067090-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.277 in 151,764 control chromosomes in the GnomAD database, including 7,083 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 0.28 (7083 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41979 AN: 151646 Hom.: 7080 Cov.: 32

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.277 AC: 41985 AN: 151764 Hom.: 7083 Cov.: 32 AF XY: 0.277 AC XY: 20500 AN XY: 74140

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.300

Alfa AF: 0.311 Hom.: 1018

Bravo AF: 0.263

Asia WGS AF: 0.364 AC: 1263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16850408; hg19: chr4-74932807;