rs7565310

Variant names:

• chr2-128386380-A-G
• rs7565310

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 0.356 in 152,168 control chromosomes in the GnomAD database, including 9,922 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 0.36 (9922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.356 AC: 54113 AN: 152050 Hom.: 9916 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.356 AC: 54146 AN: 152168 Hom.: 9922 Cov.: 33 AF XY: 0.356 AC XY: 26493 AN XY: 74394

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.380

Alfa AF: 0.363 Hom.: 13936

Bravo AF: 0.369

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565310; hg19: chr2-129143954;