chr9-21361958-G-A

Variant names:

• chr9-21361958-G-A
• rs597408

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 0.956 in 152,318 control chromosomes in the GnomAD database, including 69,628 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 0.96 (69628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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: 0.956 AC: 145445 AN: 152200 Hom.: 69567 Cov.: 32

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.956 AC: 145565 AN: 152318 Hom.: 69628 Cov.: 32 AF XY: 0.958 AC XY: 71347 AN XY: 74484

African (AFR) AF: 0.987 AC: 41028 AN: 41578

American (AMR) AF: 0.979 AC: 14983 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3403 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5180

South Asian (SAS) AF: 0.995 AC: 4801 AN: 4826

European-Finnish (FIN) AF: 0.933 AC: 9902 AN: 10614

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 63015 AN: 68022

Other (OTH) AF: 0.974 AC: 2061 AN: 2116

Alfa AF: 0.944 Hom.: 75745

Bravo AF: 0.961

Asia WGS AF: 0.993 AC: 3455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.72
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs597408; hg19: chr9-21361957;