rs1285407

Variant names:

• chr7-9226758-T-C
• rs1285407

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 0.265 in 151,776 control chromosomes in the GnomAD database, including 6,064 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 0.26 (6064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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: 0.265 AC: 40194 AN: 151658 Hom.: 6056 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.265 AC: 40210 AN: 151776 Hom.: 6064 Cov.: 32 AF XY: 0.266 AC XY: 19732 AN XY: 74170

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.291

Alfa AF: 0.326 Hom.: 19585

Bravo AF: 0.253

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1285407; hg19: chr7-9266388; COSMIC: COSV56003956;