chr21-23156493-T-C

Variant names:

• chr21-23156493-T-C
• rs1395087

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 0.134 in 151,752 control chromosomes in the GnomAD database, including 1,443 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 0.13 (1443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.16 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: 0.134 AC: 20390 AN: 151638 Hom.: 1443 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.134 AC: 20392 AN: 151752 Hom.: 1443 Cov.: 32 AF XY: 0.137 AC XY: 10145 AN XY: 74156

African (AFR) AF: 0.0913 AC: 3780 AN: 41410

American (AMR) AF: 0.135 AC: 2051 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 428 AN: 3464

East Asian (EAS) AF: 0.108 AC: 559 AN: 5162

South Asian (SAS) AF: 0.169 AC: 816 AN: 4820

European-Finnish (FIN) AF: 0.154 AC: 1609 AN: 10480

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10663 AN: 67892

Other (OTH) AF: 0.140 AC: 295 AN: 2108

Alfa AF: 0.153 Hom.: 749

Bravo AF: 0.128

Asia WGS AF: 0.130 AC: 450 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1395087; hg19: chr21-24528815;