rs2910400

Variant names:

• chr19-47890785-G-T
• rs2910400

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;