rs2044401

chr9-31669520-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 0.227 in 151,944 control chromosomes in the GnomAD database, including 3,938 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 0.23 (3938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.227 AC: 34442 AN: 151826 Hom.: 3926 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.227 AC: 34493 AN: 151944 Hom.: 3938 Cov.: 32 AF XY: 0.226 AC XY: 16767 AN XY: 74244

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.252

Alfa AF: 0.227 Hom.: 8244

Bravo AF: 0.237

Asia WGS AF: 0.135 AC: 468 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	11
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2044401; hg19: chr9-31669518;