rs13227860

Variant names:

• chr7-22114836-G-A
• rs13227860

Your query was ambiguous. Multiple possible variants found:

• chr7-22114836-G-A
• chr7-22114836-G-C
• chr7-22114836-G-T

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 0.26 in 151,938 control chromosomes in the GnomAD database, including 5,467 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 0.26 (5467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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: 0.260 AC: 39549 AN: 151820 Hom.: 5464 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.260 AC: 39570 AN: 151938 Hom.: 5467 Cov.: 31 AF XY: 0.259 AC XY: 19199 AN XY: 74254

African (AFR) AF: 0.186 AC: 7702 AN: 41424

American (AMR) AF: 0.271 AC: 4142 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1126 AN: 5162

South Asian (SAS) AF: 0.0857 AC: 413 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4093 AN: 10538

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20520 AN: 67944

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.278 Hom.: 19685

Bravo AF: 0.252

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs13227860; hg19: chr7-22154454;