7-65804997-A-G

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).

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: 0.279 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 v4.3

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;