rs2419485

Variant names:

• chr7-65804997-A-G
• rs2419485

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.28 (0 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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: 0.279 AC: 41951 AN: 150468 Hom.: 0 Cov.: 37

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.0931

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.269

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.279 AC: 42005 AN: 150586 Hom.: 0 Cov.: 37 AF XY: 0.283 AC XY: 20816 AN XY: 73548

African (AFR) AF: 0.478 AC: 19637 AN: 41120

American (AMR) AF: 0.274 AC: 4109 AN: 15022

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 527 AN: 3438

East Asian (EAS) AF: 0.430 AC: 2196 AN: 5106

South Asian (SAS) AF: 0.339 AC: 1599 AN: 4710

European-Finnish (FIN) AF: 0.222 AC: 2319 AN: 10436

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10898 AN: 67468

Other (OTH) AF: 0.269 AC: 563 AN: 2090

Alfa AF: 0.257 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.65
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs2419485; hg19: chr7-65269984; COSMIC: COSV68935415;