rs440837

Variant names:

• chr8-80549739-A-G
• rs440837

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 0.383 in 152,168 control chromosomes in the GnomAD database, including 15,631 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 0.38 (15631 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.383 AC: 58168 AN: 152050 Hom.: 15589 Cov.: 33

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.383 AC: 58265 AN: 152168 Hom.: 15631 Cov.: 33 AF XY: 0.380 AC XY: 28285 AN XY: 74378

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.386

Alfa AF: 0.248 Hom.: 9720

Bravo AF: 0.413

Asia WGS AF: 0.217 AC: 753 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs440837; hg19: chr8-81461974;