rs2910400

Positions:

• chr19-47890785-G-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 0.69 in 151,962 control chromosomes in the GnomAD database, including 36,252 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 0.69 (36252 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47890785G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104758 AN: 151844 Hom.: 36218 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.690 AC: 104848 AN: 151962 Hom.: 36252 Cov.: 31 AF XY: 0.690 AC XY: 51242 AN XY: 74286

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.649

Alfa AF: 0.682 Hom.: 75645

Bravo AF: 0.690

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2910400; hg19: chr19-48394042;