rs1410225

chr9-74693794-G-Achr9-74693794-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;