chr2-21050618-G-T

Variant names:

• chr2-21050618-G-T
• rs7575840
• ENST00000821616.1:n.240-837C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000821616.1(ENSG00000287956):​n.240-837C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,108 control chromosomes in the GnomAD database, including 5,539 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 0.26 (5539 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 39 publications found

Genes affected

ENSG00000287956 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287956	ENST00000821616.1		n.240-837C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39251 AN: 151990 Hom.: 5536 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.258 AC: 39266 AN: 152108 Hom.: 5539 Cov.: 32 AF XY: 0.255 AC XY: 18939 AN XY: 74364

African (AFR) AF: 0.151 AC: 6285 AN: 41512

American (AMR) AF: 0.302 AC: 4615 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3472

East Asian (EAS) AF: 0.123 AC: 638 AN: 5176

South Asian (SAS) AF: 0.141 AC: 681 AN: 4824

European-Finnish (FIN) AF: 0.293 AC: 3103 AN: 10578

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22275 AN: 67954

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.291 Hom.: 10044

Bravo AF: 0.257

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.32
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7575840; hg19: chr2-21273490;