rs2707520

chr7-121311090-C-Achr7-121311090-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;