11-73999841-A-G

Variant names:

• chr11-73999841-A-G
• rs7930460

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 0.241 in 151,990 control chromosomes in the GnomAD database, including 4,642 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 0.24 (4642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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: 0.241 AC: 36588 AN: 151870 Hom.: 4645 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.241 AC: 36609 AN: 151990 Hom.: 4642 Cov.: 31 AF XY: 0.246 AC XY: 18247 AN XY: 74276

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.198

Alfa AF: 0.228 Hom.: 1256

Bravo AF: 0.220

Asia WGS AF: 0.251 AC: 869 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	3.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7930460; hg19: chr11-73710886;