rs3844048

Variant names:

• chr9-129759990-G-A
• rs3844048

Your query was ambiguous. Multiple possible variants found:

• chr9-129759990-G-A
• chr9-129759990-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.573 in 152,074 control chromosomes in the GnomAD database, including 27,162 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 0.57 (27162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 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: 0.573 AC: 87094 AN: 151956 Hom.: 27152 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.573 AC: 87121 AN: 152074 Hom.: 27162 Cov.: 32 AF XY: 0.575 AC XY: 42731 AN XY: 74324

African (AFR) AF: 0.310 AC: 12840 AN: 41480

American (AMR) AF: 0.646 AC: 9876 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2759 AN: 5160

South Asian (SAS) AF: 0.654 AC: 3152 AN: 4816

European-Finnish (FIN) AF: 0.692 AC: 7316 AN: 10578

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46975 AN: 67968

Other (OTH) AF: 0.599 AC: 1267 AN: 2114

Alfa AF: 0.663 Hom.: 62743

Bravo AF: 0.555

Asia WGS AF: 0.608 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.039
DANN	Benign	0.81
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3844048; hg19: chr9-132522269;