rs2446823

chr8-94115384-T-G

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 0.122 in 152,154 control chromosomes in the GnomAD database, including 1,232 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 0.12 (1232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 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: 0.122 AC: 18583 AN: 152036 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.122 AC: 18632 AN: 152154 Hom.: 1232 Cov.: 32 AF XY: 0.122 AC XY: 9048 AN XY: 74370

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.139

Alfa AF: 0.117 Hom.: 1310

Bravo AF: 0.121

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2446823; hg19: chr8-95127612;