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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.610 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

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.606

Alfa AF: 0.571 Hom.: 9532

Bravo AF: 0.626

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2707520; hg19: chr7-120951144;