rs1562900

Positions:

• chr2-21723567-T-C

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 0.148 in 152,028 control chromosomes in the GnomAD database, including 2,179 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 0.15 (2179 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21723567T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233005	ENST00000435237.1	n.194-75790T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22379 AN: 151910 Hom.: 2160 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.148 AC: 22435 AN: 152028 Hom.: 2179 Cov.: 32 AF XY: 0.145 AC XY: 10752 AN XY: 74322

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0658

Gnomad4 SAS AF: 0.0955

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.155

Alfa AF: 0.113 Hom.: 536

Bravo AF: 0.158

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.082
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562900; hg19: chr2-21946439;