rs2171324

Variant names:

• chr18-28865075-C-T
• rs2171324

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 0.446 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.380 AC: 15749 AN: 41442

American (AMR) AF: 0.429 AC: 6540 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5150

South Asian (SAS) AF: 0.366 AC: 1760 AN: 4812

European-Finnish (FIN) AF: 0.469 AC: 4952 AN: 10556

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33908 AN: 67916

Other (OTH) AF: 0.500 AC: 1057 AN: 2112

Alfa AF: 0.487 Hom.: 56587

Bravo AF: 0.445

Asia WGS AF: 0.329 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2171324; hg19: chr18-26445040;