rs2077224

Variant names:

• chr11-62429955-C-A
• rs2077224

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 0.336 in 152,106 control chromosomes in the GnomAD database, including 8,857 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 0.34 (8857 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.336 AC: 51006 AN: 151988 Hom.: 8850 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.336 AC: 51040 AN: 152106 Hom.: 8857 Cov.: 33 AF XY: 0.330 AC XY: 24564 AN XY: 74350

African (AFR) AF: 0.291 AC: 12078 AN: 41504

American (AMR) AF: 0.332 AC: 5083 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1041 AN: 5166

South Asian (SAS) AF: 0.158 AC: 763 AN: 4814

European-Finnish (FIN) AF: 0.392 AC: 4145 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25663 AN: 67964

Other (OTH) AF: 0.331 AC: 700 AN: 2114

Alfa AF: 0.357 Hom.: 19562

Bravo AF: 0.334

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.68
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2077224; hg19: chr11-62197427;