rs2707520

Variant names:

• chr7-121311090-C-A
• rs2707520

Your query was ambiguous. Multiple possible variants found:

• chr7-121311090-C-A
• chr7-121311090-C-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 0.611 in 151,978 control chromosomes in the GnomAD database, including 30,921 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 0.61 (30921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92690 AN: 151860 Hom.: 30862 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.611 AC: 92806 AN: 151978 Hom.: 30921 Cov.: 32 AF XY: 0.600 AC XY: 44576 AN XY: 74248

African (AFR) AF: 0.900 AC: 37355 AN: 41508

American (AMR) AF: 0.482 AC: 7342 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2152 AN: 5172

South Asian (SAS) AF: 0.606 AC: 2918 AN: 4816

European-Finnish (FIN) AF: 0.424 AC: 4459 AN: 10526

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34947 AN: 67940

Other (OTH) AF: 0.606 AC: 1277 AN: 2106

Alfa AF: 0.562 Hom.: 18931

Bravo AF: 0.626

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs2707520; hg19: chr7-120951144;