rs7118412

Positions:

• chr11-103655026-A-G

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 0.471 in 151,998 control chromosomes in the GnomAD database, including 19,174 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 0.47 (19174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71560 AN: 151880 Hom.: 19166 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.471 AC: 71583 AN: 151998 Hom.: 19174 Cov.: 32 AF XY: 0.472 AC XY: 35041 AN XY: 74290

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.478

Alfa AF: 0.503 Hom.: 3055

Bravo AF: 0.451

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7118412; hg19: chr11-103525754;