rs921971

Variant names:

• chr18-60194430-T-C
• rs921971

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 0.214 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.138 AC: 5723 AN: 41554

American (AMR) AF: 0.174 AC: 2663 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3470

East Asian (EAS) AF: 0.180 AC: 935 AN: 5184

South Asian (SAS) AF: 0.346 AC: 1669 AN: 4830

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18001 AN: 67982

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.254 Hom.: 10203

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs921971; hg19: chr18-57861663;