8-89329957-A-G

Variant names:

• chr8-89329957-A-G
• rs4397449

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.99 in 152,164 control chromosomes in the GnomAD database, including 74,610 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 0.99 (74610 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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: 0.990 AC: 150550 AN: 152046 Hom.: 74556 Cov.: 31

Gnomad AFR AF: 0.978

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.979

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.990 AC: 150663 AN: 152164 Hom.: 74610 Cov.: 31 AF XY: 0.989 AC XY: 73570 AN XY: 74356

African (AFR) AF: 0.978 AC: 40621 AN: 41538

American (AMR) AF: 0.995 AC: 15178 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3465 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4781 AN: 5156

South Asian (SAS) AF: 0.979 AC: 4725 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10618

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67973 AN: 67988

Other (OTH) AF: 0.992 AC: 2097 AN: 2114

Alfa AF: 0.994 Hom.: 147396

Bravo AF: 0.989

Asia WGS AF: 0.937 AC: 3257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4397449; hg19: chr8-90342186;