rs1564330

Positions:

• chr2-4548208-A-G

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 0.443 in 151,998 control chromosomes in the GnomAD database, including 15,524 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 0.44 (15524 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4548208A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291325	ENST00000707165.1	n.621+38049A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67219 AN: 151880 Hom.: 15517 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.443 AC: 67281 AN: 151998 Hom.: 15524 Cov.: 32 AF XY: 0.446 AC XY: 33132 AN XY: 74286

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.430

Alfa AF: 0.409 Hom.: 3816

Bravo AF: 0.438

Asia WGS AF: 0.586 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564330; hg19: chr2-4595798;