rs921971

Positions:

• chr18-60194430-T-C

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 0.214 in 152,196 control chromosomes in the GnomAD database, including 3,831 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 0.21 (3831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32510 AN: 152078 Hom.: 3829 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.214 AC: 32520 AN: 152196 Hom.: 3831 Cov.: 32 AF XY: 0.210 AC XY: 15616 AN XY: 74390

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.220

Alfa AF: 0.257 Hom.: 7725

Bravo AF: 0.209

Asia WGS AF: 0.208 AC: 724 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921971; hg19: chr18-57861663;