rs16975296

Variant names:

• chr18-41770328-A-T
• rs16975296

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 0.17 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.439 AC: 18165 AN: 41422

American (AMR) AF: 0.0833 AC: 1274 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.0571 AC: 296 AN: 5180

South Asian (SAS) AF: 0.102 AC: 494 AN: 4824

European-Finnish (FIN) AF: 0.0775 AC: 822 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4247 AN: 67992

Other (OTH) AF: 0.119 AC: 251 AN: 2114

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs16975296; hg19: chr18-39350292;