rs2044401

Variant names:

• chr9-31669520-G-A
• rs2044401

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;