rs2171324

Variant names:

• chr18-28865075-C-T
• rs2171324

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 0.446 in 151,908 control chromosomes in the GnomAD database, including 15,547 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 0.45 (15547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.446 AC: 67741 AN: 151790 Hom.: 15541 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.446 AC: 67786 AN: 151908 Hom.: 15547 Cov.: 32 AF XY: 0.441 AC XY: 32735 AN XY: 74216

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.500

Alfa AF: 0.497 Hom.: 38207

Bravo AF: 0.445

Asia WGS AF: 0.329 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2171324; hg19: chr18-26445040;