rs13245899

Variant names:

• chr7-100899511-A-G
• rs13245899

Your query was ambiguous. Multiple possible variants found:

• chr7-100899511-A-G
• chr7-100899511-A-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 0.165 in 151,420 control chromosomes in the GnomAD database, including 2,451 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 (2451 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.165 AC: 24943 AN: 151330 Hom.: 2452 Cov.: 30

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.165 AC: 24952 AN: 151420 Hom.: 2451 Cov.: 30 AF XY: 0.167 AC XY: 12361 AN XY: 73926

African (AFR) AF: 0.0732 AC: 3022 AN: 41288

American (AMR) AF: 0.148 AC: 2254 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3464

East Asian (EAS) AF: 0.390 AC: 2000 AN: 5128

South Asian (SAS) AF: 0.256 AC: 1223 AN: 4784

European-Finnish (FIN) AF: 0.219 AC: 2272 AN: 10396

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12816 AN: 67858

Other (OTH) AF: 0.168 AC: 353 AN: 2096

Alfa AF: 0.183 Hom.: 8681

Bravo AF: 0.156

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.34
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs13245899; hg19: chr7-100497131;