rs281440

Positions:

• chr19-10289628-G-A

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 0.744 in 152,096 control chromosomes in the GnomAD database, including 42,444 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 0.74 (42444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113090 AN: 151978 Hom.: 42424 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.744 AC: 113157 AN: 152096 Hom.: 42444 Cov.: 32 AF XY: 0.743 AC XY: 55229 AN XY: 74340

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.771

Alfa AF: 0.775 Hom.: 52991

Bravo AF: 0.744

Asia WGS AF: 0.676 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281440; hg19: chr19-10400304; COSMIC: COSV53424152;