11-18249058-A-G

Variant names:

• chr11-18249058-A-G
• rs7130337

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.362 in 152,112 control chromosomes in the GnomAD database, including 11,904 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 0.36 (11904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.361 AC: 54945 AN: 151994 Hom.: 11869 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.362 AC: 55040 AN: 152112 Hom.: 11904 Cov.: 32 AF XY: 0.366 AC XY: 27241 AN XY: 74370

African (AFR) AF: 0.550 AC: 22843 AN: 41500

American (AMR) AF: 0.372 AC: 5682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3887 AN: 5152

South Asian (SAS) AF: 0.476 AC: 2294 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2541 AN: 10596

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16004 AN: 67970

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.279 Hom.: 11177

Bravo AF: 0.382

Asia WGS AF: 0.639 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.45
PhyloP100		-0.80
PromoterAI		-0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7130337; hg19: chr11-18270605;