rs281440

Variant names:

• chr19-10289628-G-A
• rs281440

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;