rs1285407

Variant names:

• chr7-9226758-T-C
• rs1285407

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 0.265 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.123 AC: 5098 AN: 41494

American (AMR) AF: 0.252 AC: 3827 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1223 AN: 5116

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4818

European-Finnish (FIN) AF: 0.322 AC: 3402 AN: 10574

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22753 AN: 67800

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.313 Hom.: 28612

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
PhyloP100		-0.094

Splicing

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

Other links and lift over

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