chr2-21810655-C-T

Position:

• chr2-21810655-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 0.386 in 151,950 control chromosomes in the GnomAD database, including 11,879 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 0.39 (11879 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21810655C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233005	ENST00000435237.1	n.315+11177C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58681 AN: 151832 Hom.: 11880 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.386 AC: 58707 AN: 151950 Hom.: 11879 Cov.: 32 AF XY: 0.383 AC XY: 28434 AN XY: 74224

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.347

Alfa AF: 0.363 Hom.: 14110

Bravo AF: 0.382

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495722; hg19: chr2-22033527;