11-127820580-A-C

Variant names:

• chr11-127820580-A-C
• rs7130878

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 0.161 in 150,052 control chromosomes in the GnomAD database, including 2,025 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 0.16 (2025 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.981
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 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: 0.161 AC: 24196 AN: 149928 Hom.: 2026 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.161 AC: 24208 AN: 150052 Hom.: 2025 Cov.: 33 AF XY: 0.159 AC XY: 11687 AN XY: 73386

African (AFR) AF: 0.166 AC: 6721 AN: 40452

American (AMR) AF: 0.138 AC: 2084 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 589 AN: 3362

East Asian (EAS) AF: 0.0403 AC: 208 AN: 5164

South Asian (SAS) AF: 0.173 AC: 824 AN: 4764

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10570

Middle Eastern (MID) AF: 0.229 AC: 65 AN: 284

European-Non Finnish (NFE) AF: 0.173 AC: 11640 AN: 67390

Other (OTH) AF: 0.157 AC: 326 AN: 2080

Alfa AF: 0.167 Hom.: 438

Bravo AF: 0.156

Asia WGS AF: 0.0910 AC: 318 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.47
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs7130878; hg19: chr11-127690475;