rs7565310

Variant names:

• chr2-128386380-A-G
• rs7565310

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 0.356 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.328 AC: 13638 AN: 41524

American (AMR) AF: 0.429 AC: 6565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2672 AN: 5162

South Asian (SAS) AF: 0.188 AC: 908 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3275 AN: 10588

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24036 AN: 67994

Other (OTH) AF: 0.380 AC: 804 AN: 2116

Alfa AF: 0.363 Hom.: 20890

Bravo AF: 0.369

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.61
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7565310; hg19: chr2-129143954;