rs2707461

Variant names:

• chr7-121347296-C-T
• rs2707461

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 0.255 in 152,064 control chromosomes in the GnomAD database, including 5,911 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 0.25 (5911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92

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 (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.254 AC: 38660 AN: 151946 Hom.: 5888 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.255 AC: 38721 AN: 152064 Hom.: 5911 Cov.: 32 AF XY: 0.250 AC XY: 18603 AN XY: 74334

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.229

Alfa AF: 0.215 Hom.: 2775

Bravo AF: 0.260

Asia WGS AF: 0.142 AC: 494 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	0.019
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2707461; hg19: chr7-120987350;