rs2447409

Variant names:

• chr8-139503529-G-A
• rs2447409

Your query was ambiguous. Multiple possible variants found:

• chr8-139503529-G-A
• chr8-139503529-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 0.58 in 152,064 control chromosomes in the GnomAD database, including 25,972 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 0.58 (25972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.580 AC: 88085 AN: 151946 Hom.: 25948 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.580 AC: 88151 AN: 152064 Hom.: 25972 Cov.: 32 AF XY: 0.587 AC XY: 43659 AN XY: 74332

African (AFR) AF: 0.657 AC: 27252 AN: 41472

American (AMR) AF: 0.541 AC: 8266 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3468

East Asian (EAS) AF: 0.791 AC: 4083 AN: 5162

South Asian (SAS) AF: 0.567 AC: 2732 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6379 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35670 AN: 67964

Other (OTH) AF: 0.567 AC: 1199 AN: 2114

Alfa AF: 0.553 Hom.: 4208

Bravo AF: 0.580

Asia WGS AF: 0.662 AC: 2301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.19
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2447409; hg19: chr8-140515772;