rs1410225

Variant names:

• chr9-74693794-G-A
• rs1410225

Your query was ambiguous. Multiple possible variants found:

• chr9-74693794-G-A
• chr9-74693794-G-C

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 0.632 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.632 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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.663

Alfa AF: 0.754 Hom.: 59983

Bravo AF: 0.618

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410225; hg19: chr9-77308710;