rs2171324

chr18-28865075-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;