rs16975296

Variant names:

• chr18-41770328-A-T
• rs16975296

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 0.17 in 152,106 control chromosomes in the GnomAD database, including 4,314 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 0.17 (4314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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: 0.169 AC: 25726 AN: 151988 Hom.: 4300 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.170 AC: 25784 AN: 152106 Hom.: 4314 Cov.: 32 AF XY: 0.168 AC XY: 12488 AN XY: 74372

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0571

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0775

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.119

Alfa AF: 0.125 Hom.: 354

Bravo AF: 0.185

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16975296; hg19: chr18-39350292;