9-74693794-G-A

Variant names:

• chr9-74693794-G-A
• rs1410225

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 0.632 in 151,952 control chromosomes in the GnomAD database, including 33,153 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 0.63 (33153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95973 AN: 151836 Hom.: 33138 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.632 AC: 96018 AN: 151952 Hom.: 33153 Cov.: 32 AF XY: 0.629 AC XY: 46708 AN XY: 74286

African (AFR) AF: 0.345 AC: 14266 AN: 41410

American (AMR) AF: 0.712 AC: 10863 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2603 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2224 AN: 5164

South Asian (SAS) AF: 0.782 AC: 3767 AN: 4816

European-Finnish (FIN) AF: 0.651 AC: 6855 AN: 10526

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53036 AN: 67988

Other (OTH) AF: 0.663 AC: 1400 AN: 2112

Alfa AF: 0.740 Hom.: 73608

Bravo AF: 0.618

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs1410225; hg19: chr9-77308710;