rs7122402

Variant names:

• chr11-115145587-G-A
• rs7122402

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.199 in 152,166 control chromosomes in the GnomAD database, including 3,716 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 0.20 (3716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 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: 0.199 AC: 30209 AN: 152048 Hom.: 3709 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.199 AC: 30221 AN: 152166 Hom.: 3716 Cov.: 32 AF XY: 0.203 AC XY: 15092 AN XY: 74368

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.201

Alfa AF: 0.201 Hom.: 600

Bravo AF: 0.185

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7122402; hg19: chr11-115016307;