rs7102569

Variant names:

• chr11-79473855-A-G
• rs7102569

Your query was ambiguous. Multiple possible variants found:

• chr11-79473855-A-G
• chr11-79473855-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 0.33 in 152,174 control chromosomes in the GnomAD database, including 8,401 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 0.33 (8401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.330 AC: 50112 AN: 152052 Hom.: 8383 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.330 AC: 50179 AN: 152174 Hom.: 8401 Cov.: 33 AF XY: 0.326 AC XY: 24216 AN XY: 74396

African (AFR) AF: 0.319 AC: 13262 AN: 41530

American (AMR) AF: 0.275 AC: 4207 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3470

East Asian (EAS) AF: 0.179 AC: 928 AN: 5180

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3417 AN: 10564

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24387 AN: 68000

Other (OTH) AF: 0.317 AC: 668 AN: 2108

Alfa AF: 0.339 Hom.: 5851

Bravo AF: 0.324

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.2
DANN	Benign	0.64
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs7102569; hg19: chr11-79184899;