rs7105630

Positions:

• chr11-103533134-T-C

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 0.603 in 152,034 control chromosomes in the GnomAD database, including 29,658 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 0.60 (29658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91594 AN: 151916 Hom.: 29652 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.603 AC: 91627 AN: 152034 Hom.: 29658 Cov.: 32 AF XY: 0.606 AC XY: 44982 AN XY: 74280

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.639

Alfa AF: 0.698 Hom.: 73036

Bravo AF: 0.596

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
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: rs7105630; hg19: chr11-103403862;